Martin Biology Direct 2011, 6:36
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REVIEW
Open Access
Early evolution without a tree of life
William F Martin
Abstract
Life is a chemical reaction. Three major transitions in early evolution are considered without recourse to a tree of
life. The origin of prokaryotes required a steady supply of energy and electrons, probably in the form of molecular
hydrogen stemming from serpentinization. Microbial genome evolution is not a treelike process because of lateral
gene transfer and the endosymbiotic origins of organelles. The lack of true intermediates in the prokaryote-toeukaryote transition has a bioenergetic cause.
This article was reviewed by Dan Graur, W. Ford Doolittle, Eugene V. Koonin and Christophe Malaterre.
Introduction
Biology currently lacks a robust and comprehensive
description of early evolution. We should aim to fill that
void, but in a language that operates with biology and
chemistry, not with branching patterns in phylogenetic
trees, versions of which based on informational genes
are called the tree of life. Genomes attest unequivocally
to the abundance of lateral gene transfer in microbial
chromosome history, but current thinking on early evolution is still largely couched in the conceptual framework of trees. When it comes to getting a fuller grasp of
microbial evolution, trees might be standing in the way
more than they are actually helping us at the moment,
because i) the overall relatedness of prokaryotic genomes is not properly described by any single tree, and
ii) the relationship of eukaryotes to prokaryotes is also
not tree-like in nature because the endosymbiotic origins of organelles introduces lineage mergers and
genetic amalgamation into the evolutionary process. If
we aim to deliver to science and society a complete picture of early evolution, then at some point we have to
incorporate the origin of life into the larger picture of
things, too, which means linking microbial evolution to
the elements on early Earth. Overall those are fairly tall
orders, but we have to start somewhere.
Getting a better picture of early evolution is important
for understanding our place in the larger scheme of
things. Yet the further back we look in time, the less we
know about the course of life’s history. The evolutionary
history of organisms visible to the naked eye – plants
Correspondence: [email protected]
Institut of Botany III, University of Düsseldorf, 40225 Düsseldorf, Germany
and animals – has a recurrently branching phylogeny
that can be more or less accurately represented in the
mathematical image of a bifurcating tree. Darwin’s
mechanisms of natural variation and natural selection
were inferred from observations of macroscopic life, and
those two mechanisms are still sufficient to explain the
phylogenetic history of such organisms whose evolutionary process is fundamentally tree-like in nature. Given
modern genome sequencing capabilities and computers,
the goal of realizing Darwin’s vision of a grand natural
system for those groups of multicellular organisms for
which he proposed descent with modification, is merely a
matter of time and effort (and we have the fossil record
as a helpful system of independent reference to boot).
All we have to do is to collect enough data from genomes and refine our tree-building methods sufficiently
to bring the structure of the tree of multicellular organisms into focus.
So certain is the conclusion about our ability to decipher the tree of macroscopic life that many an evolutionary biologist excitedly jumps straight to the
conclusion that the concept of a grand natural system –
the unity of bifurcating phylogeny and a natural systematics of cladistic variety – extends to all organisms
and all of evolutionary history. As one phylogeneticist
once optimistically put it “All the events of biological
evolution are played out somewhere along the branches
of phylogenetic trees“ [1]. However, those of us who are
trying to understand topics like early evolution, prokaryotic evolution and the prokaryote-to-eukaryote transition, know that evolution among microbial genomes –
our only source of genetic evidence (there is chemical
and geochemical evidence, too) for early evolution – has
© 2011 Martin; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons
Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in
any medium, provided the original work is properly cited.
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more to it than just sorting out the order of branches.
The claim that all of evolution maps to a tree is not
true, it only applies to organisms visible to the naked
eye, like in Darwin’s day. As it concerns our understanding of the evolution of microbial genomes, acceptance of
such claims about universal trees upon which all of life’s
events can be mapped – or worse, belief in their truth
[2] – is more likely to impair progress in understanding
early evolution than to promote it (for the evolution of
multicellular life, trees are fine).
Life’s early history is a process of microbial evolution,
where neither the evolutionary events linking the evolution of genes across prokaryotic genomes nor the processes linking prokaryotes to eukaryotes are strictly treelike in nature [3]. In prokaryote genome evolution, lateral gene transfer (LGT) is an important mechanism of
natural variation [4], while the prokaryote-to-eukaryote
transition involved the wholesale merger of prokaryotic
genomes via endosymbiosis [5-7]. Eukaryotes have meiosis to ensure that genes are only recombined reciprocally among individuals of the same species, prokaryotes
lack both such luxurious mating mechanisms and the
genetic lineage purity that they confer [8]. Prokaryotes
live in a world where plasmids hop around without
respect to systematic categories [9], where individual
cells are outnumbered 10:1 by alien infectious agents
(phage) that can enter their bodies and insert new genes
[10]; they live in a world where some individuals, faced
with a stressful life situation, cut up their genomes into
a thousand little pieces, package the 4.5 kb genome
pieces in protein and toss them into the enviroment as
gene transfer agents (GTAs) “in hope” that “someone’
will be able to use them [11,12]. Fortunately, daily
human experience is deviod of analogous processes: we
are not constantly surrounded by ten grape-sized gene
injectors that are out to convert our internal organs into
intruder copies, and when we feel stressed, we do not
saw off our toes and offer them to our neighbors.
When we study the long-term evolution of things like
birds and bees and flowers and trees, we can confidently
lean on the concept of a tree and safely assume that biological events play out along the branches of a bifurcating phylogeny (of populations). But when we study
prokaryote evolution, where LGT abounds, or the prokaryote-to-eukaryote transition [13], which centrally
involves the origin of mitochondria and gene transfers
to the nucleus[12-15], the processes at hand are not
tree-like to begin with.
Taught tradition in evolutionary biology implores us
to approach, understand and converse on lineage history
in terms of trees. But for microbes, trees are not enough
if we want to understand genome evolution [16]. Each
gene in a given prokaryotic genome has its genealogical
tree, yes, but the farther we go back into evolutionary
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history, the less congruent are the trees of different
genes, and the farther we look across prokaryotic diversity, the smaller is the fraction of genes whose distribution across genomes is accounted for via vertical
descent. If we want to depict the evolution of prokaryotes, trees are inadequate because they capture only a
tiny amount of the underlying evolutionary dynamics.
The tree of life as currently defended [17] is more about
classification and the search for a tiny minority of genome data that might be treelike over some portions of
history – though is it very difficult to show that they are
treelike [18] – than it is about understanding microbial
evolutionary dynamics. As some of us have said before:
microbial evolution and the tree of life are two different
things [8].
This realization has (or should have) two consequences. First, it puts an onus upon us to divorce the
study of microbial evolution from a rigid manifesto of
natural systematics, which is simple enough [3,19]. Second, it puts an even heavier onus upon us to react in
our methods of investigation of, and our conceptual
approach to, microbial evolutionary processes by resorting to the use of mathematical models that are more
complex than the simple bifurcating tree. Of course, it
is not absolutely imperative that we react. We can, if we
so choose, simply pretend that microbial evolution really
is tree-like after all [2,17] and impose the bifurcating
tree on our thinking at all levels so that we can ask
questions of which bifurcations fit our favorite natural
categories better, without daring to ask whether the
underlying process going on in nature is tree-like to
begin with.
If, however, we choose to react with our repertoire of
analytical methods, then the obvious solution is to pursue network-based, rather than tree-based, approaches
to the study of microbial genome relatedness. In the
realm of networks, we can concern ourselves with questions of how to model, in mathematical terms, the
microbial evolutionary process – for example non-directed [20,21] vs. directed [22] networks – but we do not
need to worry immediately about the implications for
systematics, which for prokaryotes or phages [23] can
hardly be strictly natural anyway, because of lateral
transfer. Networks do not confine our thinking to the
preconcieved notion that microbial evolution corresponds solely to a process of pure clonal lineage splittings that, over time, generate the patterns of
recurrently bifurcating trees.
The tree of life is only one impediment to a better
understanding of early evolution
If we want a full picture of evolutionary history, we have
to look all the way back to life’s origin. As the major
evolutionary transitions, Maynard Smith and Szathmary
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[24] listed: i) the origins of replicating molecules in
compartments (from replicating molecules), ii) chromosomes (from independent replicators), iii) DNA and protein (from RNA), iv) eukaryotes (from prokaryotes), v)
sexual populations (from asexual ones), vi) multicellular
life (from protists), vii) colonies (from individuals), and
viii) human societies (from primate predecessors). Half
of the major transitions they identified fall in the realm
of early evolution. Lane [25] lists the ten major inventions of evolution as encompassing the origins of i) life,
ii) DNA, iii) photosynthesis, iv) eukaryotes, v) sex, vi)
motility, vii) sight, viii) warm bloodedness, ix) consciousness and x) death. He also sees half of evolution’s
greatest inventions within the realm of early evolution.
Koonin [26] lists the origins of i) protein folds, ii)
viruses, iii) prokaryotic cells, iv) the major prokaryotic
groups, v) eukaryotes and vi) animal phyla as the major
evolutionary transitions, again mostly falling within the
realm of early evolution. That does not necessarily mean
that more interesting things happened during early evolution than later, but perhaps that we just wish that we
knew as much about early evolution as we know for
events later in evolution.
From my perspective, the three most important processes (only two of which are evolutionary transitions)
in early evolution are i) the origin of life, ii) prokaryotic
evolution, and iii) the prokaryote-to-eukaryote transition. Traditionally, those are the areas where evolutionary biology’s greatest weaknesses have been when it
comes to providing a fully tangible account of life’s history. One might ask: Is it important for evolutionary
biology to provide a better understanding of the very
earliest history of life? It is arguably one of the most
important frontiers facing science, specifically as evolutionary biology interfaces with society. One might also
ask: Can we ever understand anything as complex as the
origin of life and early evolution? The answer is unquestionably yes, the issue is merely when we will attain that
understanding.
But much like pulling teeth, making progress on these
issues can mean that we have to let go of one or the
other of our familiar and trusted theories (or elements
thereof) from time to time, which can be painful (but
like a visit to the dentist, things generally feel better
afterwards). The alternative needs to explain more or as
much of the same observations while requiring fewer
corollary assumptions (we want better teeth, not fewer).
That said, three major obstacles to progress in the field
of early evolution can currently be identified, views that
served well in their day but that now need to go. These
impediments concern three traditional and widely held
– but if we think about it in more detail, untenable –
notions about the course of early evolution that are deeply engrained in the minds of scientists and society and
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that we must abandon altogether if we are to make
headway on these central issues. The three conceptual
impediments are the notions that: i) life arose from
some kind of organic soup, ii) microbial evolution has
anything to do with a tree of life or otherwise has the
shape of a tree, and iii) the prokayote-to-eukaryote transition occurred before the origin of mitochondria (as
opposed to the more easily defendable view of its having
ocurred in the wake of the origin of mitochondria).
Life is a chemical reaction, not stirred organic soup
The very familiar concept that life arose from some kind
of organic soup is 80 years old [27-29] and had best be
abandoned altogether. The reason is that life is not
about the spatial reorganization of preexisting components, it is a continuous chemical reaction, an energyreleasing reaction, and a far-from-equilibrium process.
The proposal that life arose through the self-organisation of preformed constituents in a pond or an ice-pore
containing some kind of preformed prebiotic broth can
be rejected with a simple thought experiment: If we
were to take a living organism and homogenize it so as
to destroy the cellular structure but leave the molecules
intact, then put that perfect organic soup into a container and wait for any amount of time, would any form
of life ever arise from it de novo? The answer is no, and
the reason is because the carbon, nitrogen, oxygen, and
hydrogen in that soup is at equilibrium: it has virtually
no redox potential to react further so as to provide electron transfers and chemical energy that are the currency
and fabric of life [30-32].
If not soup, what? Life is about redox chemistry, so
the site and environment of life’s origin should be
replete with redox reactions. Alkaline hydrothermal
vents provide a good model for understanding early chemical evolution because they have some similarity to living systems themselves. Perhaps similar to some types
of hydrothermal vents observable today, such as Lost
City [33-36], alkaline vents during the Hadean would
have offered a necessary and sufficient redox potential
(in the form of the H2-CO2 redox couple) and catalytic
capabilities (in the form of transition metal ions) to permit organic synthesis at a specific location in space and
stably over geological time to give rise to the chemical
constituents of life and to foster the transition from geochemically contained chemical networks to bona fide
free-living cells [30-32]. Why, exactly, are alkaline
hydrothermal vents conceptually attractive in the origin
of life context? There are a number of reasons, many of
which are old as the discovery of vents themselves
[37,38] but they remain current [39].
One reason concerns compartmentation. Compartmentation from the environment is essential for the
transition from inorganic matter to the first living
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systems [30,31,40,41], and hydrothermal vents are
replete with naturally forming microcompartments
[30,34], geochemically formed concentrating mechanisms to enable the origin of replicating systems. Let’s
recall that replication means doubling of mass, hence
the precursors for any doubling need to be in steady
supply, ideally at their site of synthesis.
A second reason concerns thermodynamics. Life cannot have emerged against the laws of thermodynamics.
Excitingly, the overall reaction for the synthesis of the
chemical constituents of a microbial cell is exergonic
(energy-releasing) at temperatures of around 50-100°C,
as recent calculations show [42] for exactly the kind of
alkaline hydrothermal vent (chemically similar to Lost
City) that some of us have in mind [39]. In other words,
the synthesis of life’s substance (protein, nucleic acids,
cell wall, lipids, etc) from the concentrations of CO2 ,
H2S, HPO42-, NH4+, H+ and electrons (H2) as would be
found at the vent ocean interface of such an alkaline
hydrothermal system releases energy, even without considering main energy metabolic reactions, just considering anabolic cell mass accumulation [42]. That is very
important because most people assume that at life’s origin one had to add a special kind of energy somehow
(for example in the form of lightning), rather than harnessable chemical energy being available naturally, all
the time.
In addition there is the nature and availability of that
chemical energy to consider. The most obivious source
of energy for early chemical and living systems, and
the kind considered by Amend and McCollom [42] is
molecular hydrogen, H 2 , steming from geochemical
processes, just as are observed at Lost City today [36].
Lost City effluent contains about 10 mM H2 [36]. H2,
both from geological sources [43] and from biological
sources [44] is very widely used by prokaryotes as a
source of electrons and energy today [45]. But H2 is so
simple that it is often overlooked: a recent review of
the possible sources of energy for the origin of life
does not mention H2 at all [46], even though it is the
most abundant source of accesible chemical energy on
the early Earth [47] and arguably the far most likely
source of energy for the first prokaryotic cells [32,48].
Where does that H2 come from? It comes from a process called serpentinization [47,48]. In submarine
hydrothermal systems, seawater circulates through the
cust. It is drawn into the crust by gravity through
cracks in the rock to depths of ~3 km where it is
heated to about 150-200°C (because the deep crust is
warmer than the surface). The water undergoes a
redox reaction with the vast amounts of Fe 2+ in the
crust. Water is reduced by Fe 2+ to H 2 , which ultimately emerges in the hydrothermal effluent, yieding
oxidized iron, Fe3+, in the form of Fe3O4 [47,48].
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Enter the ominous issue of the origin of chemiosmotic
energy coupling. The process of serpentinization also
makes the effluent alkaline, and Lost City effluent is
about pH 10 [33,43]. Why is that significant? Figure 1
depicts the problem. If we look around in biology very
hard, and consult very knowledgeable bioenergeticists
[49] to make sure, we find that there are only two ways
that energy is conserved in the form of ATP among life
forms that we know: chemiosmosis [50] entailing rotorstator type ATPases and substrate level phosphorylations. That is very significant. It is also a very carefully
worded sentence because a new mechanism of energy
conservation has recently been discovered in strict anaerobes that does not involve the phosphoanhydride bond
in ATP. It involves the synthesis of reduced ferredoxin
– an energy rich compound – coupled to a second exergonic redox reaction. The coupling mechanism is called
electron bifurcation, because electron pairs are spilt in
the reaction mechanism, which entails a flavin cofactor
[51-53].
The only organisms that do not use ATPases for their
energy conservation are pure fermenters, who gain their
energy through the disproportionation of reduced carbon compounds. But those reduced carbon compounds
are made by autotrophs, either photoautotrohs or chemoautotrohs, which always – without known exception
– use chemiosmotic coupling mechanisms. Moreover,
pure fermenters are always derived from chemiosmotic
ancestors. Chemiosmosis is the ancestral state of ATPdependent energy harnessing among free-living cells
[54]. Chemiosmotic energy coupling has two components. The first is a membrane-bound multisubunit
rotor-stator type ATPase (called F-type in eubacteria
and A-type in archaebacteria, the F- and A- types are
structurally similar and related). The second is a membrane bound protein-cofactor system that performs a
redox reaction of the type D red + A ox ® D ox + A red
(whereby D and A stand for electron donor and acceptor, respectively [50]) the vectorial orientation of whose
components across the membrane results in cations,
usually protons, being removed from the cytosol and
deposited outside the cell, making the inside of the cell
alkaline relative to the environment. The origin of this
ancestral state of energy harnessing, as universal as the
genetic code, is usually but not always [30] disregarded
altogether in the early evolution literature, as Mike Russell has repeatedly pointed out. The ion-pumping
machinery is extremely variable across prokaryotes,
whereas the ATPase is conserved. Which came first?
Today, the two components are dependent upon each
other to provide a functional unit. In the early evolution
of life at an alkaline hydrothermal vent, the ATPase (a
protein) could have harnessed the naturally preexisting
proton gradient (roughly pH 9 inside, roughly pH 6
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1. Chemiosmosis, Peter Mitchell (1961)
H+
H+
H+
H+ H+
H+
Ared
ADP + Pi
ATP
Aox
H+ H+
+
H
H+
H+
Dox
useable
chemical energy
H+
e–
Dred
2. Fermenters (derived from chemiosmotic types)
Figure 1 The two ways that cells conserve energy in the form of ATP (note that some energy conservation in anaerobes involves
ferredoxin instead of ATP [51-53]): 1) chemiosmosis and 2) substrate-level phosphorylation. The figure shows a schematic representation
of chemiosmotic energy harnessing [50]. A redox reaction (left) is used to channel electrons though plasma membrane-associated proteins and
cofactors in such a way that protons are depleted in the cytosol, creating a chemical and electrochemical gradient. Return of the protons to the
cytosol occurs through an ATP synthase (ATPase), where ATP is synthesized from ADP and Pi. D donor, A acceptor, red reduced, ox oxidized. In
rhodopsin-based photosynthesis, the protons are pumped without redox reactions, but in the absence of redox chemistry, no cell can survive.
See references [49-53].
outside [30,32,48]), at the vent ocean interface (Figure
2). That would directly account for the circumstance
that the ATPase and the principle of harnessing ion gradients across the prokaryotic plasma membrane is universal and far more conserved than i) the components
that generate the ion gradient and ii) even the chemical
constituents of membranes themselves, if we consider
the breadth of prokaryote diversity. One might ask how
then early chemical systems conserved any chemical
energy at all prior to the advent of chemiosmotic coupling (which requires genes and proteins). The suggestion is that H2-, CO2-, and methyl-dependent (perhaps
methylsulfide) substrate level phosphorylations were the
initial source of chemical energy, leading to acyl
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using a natural proton gradient
H+
Vent
pH ~9
Ocean
H+
pH ~6
Hydrothermal flux
H+
ATP
H+
H+
H+
H+
ADP + Pi
H+
energy
pH ~9
H+
H+
H+
H+
H+
ATP
H+
H+
H+
ADP + Pi
H+
H+
Figure 2 An alakaline hydrothermal vent harbours a natural proton gradient. The flux of hydrothermal effluent maintains an alkaline
interior. In the presence of appropriate proteins, this source of energy could, in principle, be tapped. The harnessing of naturally preexisting
chemiosmotic gradients before the advent of genetically specified mechanisms to generate such gradients would directly explain why ATP
synthases of the F-type (eubacteria) and A-type (archaebacteria) are universal and conserved [63], but the mechanisms to generate proton
gradients are not. See references [30-32,48].
phosphates such as acetyl phosphate that were the first
broadly available energy currency for biochemical evolution at the vent up to the level of genes and proteins
[32]. Acyl phosphates still have a very broadly distributed and central role in prokaryotic energy metablic processes today [55].
The abiotic (geochemical) synthesis of simple organic
compounds at Lost City today provides exciting clues as
to what kinds of chemistry the early Earth might have
had in store. Lost City effluent contains about 1 mM
methane with an isotope signature that indicates an
abiotic origin, probably through reduction of dissolved
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CO2 via serpentinizarion [36]. Although a minor component of the methane might be of biological origin, the
vast majority is of geochemical origin [56]. Short
alkanes, up to pentane, of abiotic origin are also
detected, as is (significantly) formate (about 0.1 mM)
[57]. This indicates that geochemical processes can
indeed produce compounds relevant for biochemistry,
very much in line with predictions of the view that life
arose in such environments. The smaller amounts of
acetate in Lost City effluent (about 0.01 mM) appear at
present to be of biological origin [57]. One might like to
see evidence for the abiotic synthesis of more complex
organic compounds in Lost City efluent, but one needs
to recall that the subsurface biosphere is a vast [58] and
hungry community, and if anything organic of much
direct microbial use is synthesized geochemically, the
chances are good that it will be consumed before the
effluent reaches the surface. That circumstance (the prokaryotic colonization of the deep subsurface) is perhaps
the biggest difference (apart from abundant O2, sparse
CO2 and lacking Fe2+ in modern ocean water) between
chemistry at a Lost City type vent today and what might
have been going on in a similar system during the
Hadean.
The kinds of microbes inhabiting Lost City are mainly
methanogens (and anaerobic methane oxidizing forms
thereof) [43]; one can only speculate about the possibility of more deeply inhabiting acetogens, based on effluent acetate concentrations [57], and recalling that Lost
City effluent is rich in H2 but devoid of detectable CO2
[43,57]. Methanogens and acetogens generate their ATP
chemiosmotically during the process of synthesizing
reduced organic compounds for biosynthesis [59,60].
Chemically they have more in common than their genes
might suggest [32]. Significantly in my view, both acetogens and methanogens are known that lack cytochromes, and these forms generate their chemiosmotic
potential without the help of either quinones or methanophenazine (the functional analogue of quinones in
methanogens) [59,61]. Chemiosmotic pumping without
the use of quinones or their analogue is generally rare
in biology, simpler (requiring many fewer genes) than
cytochrome-dependent chains, and arguably the most
primitive state of proton-pumping machineries. That the
corresponding ion-pumping complexes of cytochromelacking methanogens (a methyltransferase, the MtrA-H
complex [53,59]) and of cytochrome-lacking acetogens
(a ferredoxin:NADH oxidoreductase, the Rnf complex)
[61,62] are unrelated is not surprising, as these represent, in this view, independent molecular solutions to
the problem of how to generate a proton gradient (how
to replace the naturally preexisting one at an alkaline
vent) with a chemistry that is specified by genes.
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It is also noteworthy that the methanogens (archaebacteria) and acetogens (eubacteria) share chemically
related but genetically distinct versions of the acetylCoA pathway of CO2 fixation and the distinction of living from some of the smallest redox potentials known
to fuel free-living cells [63]. The biochemistry of acetogens and methanogens appears to have enough in common with geochemistry at alkaline vents to make the
case that they are homologous (related via common
ancestry) [32]. Are molecular data in any way compatible with that view? Evidence, albeit based in trees, was
presented by Kelley et al. [64] “for a methanogenic origin
of the Archaea“. For acetogens (taxonomically, clostridias and relatives, Firmicutes, or low GC Gram positive
bacteria) similiar tree-based evidence for their basal
position among eubacteria has been presented: “In our
tree, Firmicutes are placed at the earliest division of
Eubacteria with 66% BP support, and 33% of remaining
BP show at least a subclade of Firmicutes at the earliest
division“ [2]. There is no reason to get too excited about
that, because the results are based in trees, but it is
worth noting that the results come out this way. Genomes from Clostridia (and Thermotoga) lineages also
draw attention to the origin of their ancient traits [65],
though not in the context discused here.
The view that the acetyl-CoA pathway is the ancestral
state of microbial carbon and energy metabolism suggested an important role for chemically accessible
methyl groups, for example methyl sulfide, at the orgin
of biochemistry [32]. It has since become apparent that
methyl sulfide is an important intermediate in modern
microbial interactions involving methanogens [66]. The
harnessing of a prexisting proton gradient at the vent
ocean interface clearly suggests that protons were the
ancestral substrates of ATPases. Mulkidjanian and colleages [67] examined ATPase sequences and came to
the conclusion that sodium might be the ancestral substrate, but they also noted that their conclusion is contingent on the premise that the same set of ligands
conferring Na + specifiity over H + specificity did not
arise through convergent evolution. It turns out that
“the same set of ligands” boils down to two amino acid
substitutions in the membrane portion of the enzyme
[67], whereby the convergent emergence of two amino
acid substitutions is a commonplace observation even
during human mitochondrial DNA evolution [68], so
the view that protons were the ancestral substrate of
ATPases is compatible with available data. Like the
acetyl-CoA pathway, the newly discovered mechanism
of energy conservation entailing electron bifurcation and
cytoplasmic ferredoxin pools, which is arguably ancient
[51], is found in both clostridias [52] and methanogens
[53], compatible with the premisses set forth above.
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At depth, the tree of life is not a tree
The second concept about early evolution that we need
to abandon is the notion that the overall course of prokaryotic evolution can be accurately described using the
mathematical model of a bifurcating tree as a model for
the evolution of chromosomes. This point, namely that
prokaryotic evolution is not a tree, has been argued
often enough in these pages [8] and elsewhere [69]. The
nature of the main arguments has not changed much in
the meantime. Prokaryote evolution is not treelike
because lateral gene transfer (LGT) is a real and prevalent mechanism of natural variation among prokaryotes
[3]. Genomes sequences have revealed that over evolutionary time, prokaryotic genomes undergo LGT, the
known mechanisms of which entail acquisition through
conjugation, transduction, transformation, and gene
transfer agents in addition to gene loss [70-72]. This
leads to different histories for individual genes within a
given prokaryotic genome and networks of gene sharing
across chromosomes among both closely and distantly
related lineages. In genome comparisons, LGT is traditionally characterized in terms of conflicting gene trees
[73,74] or aberrant patterns of nucleotide composition
[75]. But in the larger picture of genome evolution, a
tree can account for only about 1% of prokaryotic evolutionary history at best [18,76].
If not a tree, what then? Networks should, in principle, be able to more fully uncover the dynamics of prokaryotic chromosome evolution. Networks are currently
used to model various aspects of biological systems such
as gene regulation [77], metabolic pathways [78], protein
interactions [79], conflicting phylogenetic signals [80,81],
and ecological interactions [82]. Although it is obvious
that a network analysis of gene distributions across prokaryotic genomes should provide a more realistic view
of microbial evolution, one that incorporates the contribution of LGT into the process, if we look to the literature, the field is mostly still using trees [83], although
evolutionary networks are actively being used as well
[9,20-23,84,85], opening up many new and fruitful interdisciplinary avenues of pursuit. The use of networks
instead of, and in addition to, trees should lead to a
change in the way that microbiologists approach the
process of prokaryote genome evolution.
Biologists and philosophers recently inspected the tree
of life concept, unearthing a multitude of insights and a
plurality of views [86-97]. In that discourse, nobody
came out in favor of the concept of a single unified
bifurcating tree (and classification system) as the Rosetta
stone to life’s history, with most contributors pointing
to the circumstance that the processes operating in early
evolution are not strictly treelike, because of endosymbiosis and because of LGT, which some of us have been
saying all along [98,99]. So who, if anyone, is actually
Page 8 of 25
defending the tree anymore? The most stalwart defence
of the tree of life in recent years came not from biologists, but from a historian [100], and it could be that the
most tree-prone among microbiologists would defend
the method of using trees to study microbial evolution
more vociferously than they might defend any particular
tree itself [17]. As leaves and branches in the tree of life
come and go, new approaches to the analysis of genome
data will continue to emerge, some of which will be
based neither on trees nor on networks [101]. It is unlikely that we will still be reading the history of microbial
evolution in 20 years time from the order of branching
patterns on a tree, as some would like to do it today [2].
Over time, networks will probably come to play an
increasingly important role in the study of prokaryote
evolution and the prokaryote to eukaryote transition.
The place of eukaryotes in the bigger picture
Related both to the origin of life issue and the tree of
life issue is the place of eukaryotes in the bigger picture
of evolution. From the standpoint of the genome
sequence comparisons, eukaryotes are genetic chimaeras
with archaebacterial type ribosomes in the cytosol, a largely archaebacterial-type information processing
machinery and eubacterial-type energy production and
metabolic machinery. Lake [102] termed this general
functional dichotomy, with its characteristic pattern of
conserved sequence similarity, informational and operational genes. This genetic and functional chimaerism in
eukaryotes is well documented [5-7,103]. Although there
are many theories for the origin of eukaryotes, each
designed to account for different aspects of eukaryote
biology [reviewed in [104]], only three basic theory varieties address this general pattern of sequence similarity
in eukaryotic genomes.
The first is an element of the neomuran theory of
eukaryote origins [105,106] called “quantum evolution”
[107], a kind of gene-class-and-lineage-specific evolutionary rate fluctuation that is assumed without logical
penalties to explain any pattern of observed sequence
similarity (or lack thereof). In that view, eukaryotes and
archaebacteria arose from actinobacteria less than a billion years ago. Diverging from their common ancestor,
the ancestral stem eukaryote became phagocytotic, while
the ancestral stem archaebacterium invented things like
methanogenesis and everything else that distinguishes
archaebacteria from eubacteria (this imaginatively late
origin of methanogenesis conflicts with copious geochemical data [32]). The genes showing strong similarity
between eukaryotes and archaebacteria – but not to
eubacteria (informational genes) – underwent a radical
kind of fast and furious molecular evolution over a
short period of time that created that pattern, while the
genes showing strong similarity between eukaryotes and
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eubacteria – but not to archaebacteria – underwent a
similarly radical kind of fast and furious evolution in the
common ancestor of all archaebacteria [107]. Because
the theory operates with rate fluctuations to explain
molecular sequence similarites, it can hardly be tested
or supported with molecular data. One might complain
that genome data link neither eukaryotes nor archaebacteria to actinobacteria, even though that evolutionary
transition is only supposed to have occurred 850 MY
ago under the theory. However, the nature of the supposed underlying evolutionary process (quantum evolution) erases that sequence similarity trace, for which
reason scientific criticism of the theory can be frustrating. As in earlier versions of the theory that derive
eukaryotes from cyanobacteria [108], the origin of phagocytosis is seen as the crucial evolutionary invention en
route to the eukaryotic state [106], an old idea [109]
that still has distinguished supporters today [110]. The
earliest-branching eukaryotes in the phagotrophic theory
were once called archezoa [111], a taxonomic group
that has long since disappeared from the literature,
unlike the phagotrophic theory [102] that generated it.
While many of the eukaryotic taxonomic groups put
forth by Cavalier-Smith have proven robust, his
accounts of the prokaryote to eukaryote transition have
remained problematic.
In the age of genomes, even supporters of the phagotrophic theory had to account for the circumstance that
eukaryotes had archaebacterial informational genes, but
preferably without extensive and specific rate fluctuations of gene and protein sequence evolution of the
quantum evolution type hard-wired into the theory.
Hence a second and popular solution to the origin of
informational and operational genes was to suppose that
there was some kind of archaebacterial endosymbiont in
eukaryote evolution, presumably one that gave rise to
the nucleus, usually presumed to have arisen in a eubacterial host. Several variants on this theme emerged
[112-118], and continue to emerge [119]. Those theories
have at least three major problems in common. First,
and in contrast to chloroplasts and mitochondria, the
nuclear compartment is in no way homologous to a prokaryotic cell, hence the whole (100 year old) notion that
the nucleus was ever an endosymbiont is tenuous to
begin with [120]. As with the flagellum [121] or microbodies [122], there is no evidence or homology at all to
suggest that the nucleus is descended from an symbiotic
bacterium. Second, they derive a cell that has eubacterial
genome and eubacterial ribosomes in the cytosol, with
the informational genes locked up within the archaebacterial endosymbiont. No formulations of nucleosymbiotic origins to date, even the most recent [119], provides
any sound rationale as to how we arrive at a state where
the ancestral eubacterial ribosomes and genome in the
Page 9 of 25
cytosol are gone and the archaebacterial ribosomes are
operating in the cytosol while the archaebacterial chromosomes are retained in the nucleus. Third, theories for
an endosymbiotic origin of the nucleus suffer, like the
phagotrophic theory, from the circumstance that they all
educe, as their crucial intermediate, a eukaryote that primitively lacks mitochondria (an archezoon), thereby predicting that primitively mitochondrion-lacking groups
should still be around today. Contrary to that prediction,
it has turned out that all eukaryotic groups either once
possessed or still possess mitochondria, either in the
form of O2-respiring mitochondria, anaerobic mitochondria, hydrogen-producing mitochondria (hydrogenosomes) or highly reduced mitochondria (mitosomes)
[123-129]. Nucleosymbiotic origin theories keep cropping up in new garb, probably because none of them
really account for the observations and remain unconvincing, sometimes even to their proponents [119].
As the third kind of theory that can account for the
informational operational classes of eukaryotic genes,
some of us have suggested that the host for the origin
of mitochondria was simply an archaebacterium. A couple such theories have been proposed [130,131], one of
which also directly accounted for the common ancestry
of mitochondria and hydrogenosomes and explicitly predicted that all eukaryotes lacking typical mitochondria
had secondarily lost them [132]. Under that view, called
the hydrogen hypothesis, the host was a H2-dependent
archaebacterium and the endosymbiont was a facultatively anaerobic eubacterium, the common ancestor of
mitochondria and hydrogenosomes, whose ability to
perform anaerobic H2-producing fermentations (in addition to respiration) provided the selective pressure initially associating the symbiont to its host. The
archaebacterial nature of the eukaryotic genetic apparatus is readily explained via direct descent from the
archaebacterial host, while the eubacterial nature of
eukaryotic energy metabolism is directly accounted for
via endosymbiotic gene transfers [133] from the genome
of mitochondrial endosymbiont to the chromosomes of
the host, resulting in the genetic displacement (and chimaeric nature) of many preexisting host pathways [132].
The origin of the nucleus in this mitochondrion-bearing host appears to be linked to the origin of introns
and spliceosomes [134] from group II introns of mitochondrial origin that hitchhiked into the host chromosomes during the course or gene transfer. These mobile
prokaryotic introns spread to many positions in the genome, and underwent the transition to spliceosomal
introns at those ancient eukaryote intron positions.
Because ribosomal translation is faster than spliceosomal
splicing, the host would only be able to express its
(many) intron-containing genes by doing away with the
prokaryotic paradigm of cotranscriptional translation
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Page 10 of 25
(Figure 3). That is, a separation of splicing from translation became imperative for survival (extinction also
being an option). Accordingly only such descendants
survived that were able to separate splicing from translation by exclusion of ribosomes from the space
surrounding active chromatin. Separation in cells usually
involves membranes, and this offers a mechanistic rationale that can readily account for the observations that
the only cells that ever evolved spliceosomes (eukaryotes) also evolved a nuclear membrane (composed of
The origin of the nucleus.
Group II introns spread to many sites in the host’s chromosomes
and undergo the transition to spliceosomal introns at many positions.
This causes problems because
i. ribosomes
are fast,
ii. spliceosomes
are slow,
iii. hence gene expression is severely impaired.
A dedicated
translation
compartment
Cytoplasm
Nuclear
membrane
Slow splicing can
go to completion
Nucleoplasm
Ribosome
Intron (DNA)
Intron (in mRNA)
Spliced intron
RNA polymerase
Exon (DNA)
Spliceosome
Nascent protein
on ribosome
Figure 3 The origin of spliceosomal introns precipitated the origin of the nuclear membrane in a mitochondrion bearing cell. See
reference [134].
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eubacterial lipids) and had (group II intron containing)
mitochondria as well [134]. Compatible with that view,
group II introns are indeed still mobile in prokaryotes
today [135] and nuclear expression of group II introns
yields a splicing behaviour that is very consistent with
the predictions of the model [136]. In addition,
sequenced eukaryotic genomes are replete with evidence
for ongoing gene transfers from organelles to the
nucleus today [137,138]. This view for the autogenous
origin of the nucleus in a mitochondrion-bearing cell
also directly accounts for the observation that eukaryotes have their chromosomes and splicing in the
nucleus, their archaebacterial ribosomes in the cytosol
and their eubacterial ribosomes in the mitochondrion.
While it is easy to conjure up scenarios for the origin
of eukaryotes that are more complicated and involve
more partners [112-119] than models involving an
archaebacterial host, there are no simpler scenarios, and
this simplicity is a virtue of the theory. The only way to
invoke fewer cellular partners than an archaebacterial
host and a mitochondrial endosymbiont at eukaryote
origins [5,129,132] requires reverting to the view that
mitochondria did not arise via endosymbiosis [108].
Critics sometimes complain that the eubacterial genes in
eukaryotes do not all trace to a-proteobacterial homologues [114,119], but if we incoportare LGT into the bigger picture of genome evolution then it becomes
untenable to assume that the ancestor of mitochondria
either i) had a pristine genome devoid of “non-a-proteobacterial” genes at the time of endosymbiosis (whatever
an a-proteobacteral gene is) or ii) that its free-living
descendants never underwent gene donations to, or
gene acquisitions from, other prokaryote lineages. In
this way, LGT among free-living prokaryotes readily
accounts for the apparent eubacterial mosaicism of
eukaryotic nuclear genomes via the sample of genes that
eukaryotes acquired at the origin of mitochondria
[12,99].
Despite the circumstance that prokaryotes can harbour other prokaryotes as endosymbionts [25,139] and
despite evidence for multiple origins of phagocytosis in
eukaryote evolution [140] some maintain the position
that phagotrophy, rather than the origin of mitochondria, just absolutely has to be the first step in the prokaryote to eukaryote transition [106,110]. Whole
theories rest on the argument that the only way that a
eubacterium can enter another cell to become an endosymbiont is if the host is phagotrophic, sporting staunch
quotes: “Phagocytosis by a protoeukaryote host is the
only viable mechanism currently available to explain the
origin of the mitochondrion” [141]. If the phagotrophic
argument held any strength, then the existence of bacterial endosymbionts – in prokaryotes, above, and – in
fungi would be an impossiblity, because fungi do not
Page 11 of 25
phagocytose. Well, it turns out that endosymbionts in
fungi are common [142] and that in fact, “Bacteria that
inhabit fungi intracellularly, or endosymbiotically, have
been described for more than three decades. Endosymbiotic bacterial fungal interactions are ubiquitous and have
been documented from all parts of the world“ [143]. So
much for (the origin of) phagocytosis being required for
the establishment of intracellular endosymbionts.
The extreme stance that eukaryotic cell organisation
(and phagocytosis) is ancestral to that in prokaryotes in
general [144], is an issue that would appear, in a tree of
life mindset, to hinge on branching orders deep in the
tree of life [145]. But in this paper we are addressing
early evolution without a tree of life and hence wish to
approach the issue in a manner that does not hinge
upon branches, the abundance of endosymbionts in
non-phagocytosing hosts notwithstanding.
For phagocytosis, a cell requires complex machinery of
membrane traffic mechanisms: an endoplasmic reticulum, Golgi, actin/tubulin cytoskeleton, cytokinesis, vesicle fusion mechanisms, phagosome formation,
exocytosis, etc. That is a considerable level of evolutionary invention, entailing the origin of ~2000 new proteincoding genes [146]. For bioenergetic reasons, the origin
of that machinery and its expression as protein requires
mitochondria [147]. Prokaryotes have remained prokaryotes for > 3 billion years because they lack mitochondria. The increased energy per host gene that
mitochondria confer upon their host by virture of vast
bioenergetic membrane surface area, and bioenergetically specialized genomes (mtDNA) to service it
[13,147,148], was strictly required to finance, in energetic terms, the origin of eukaryotic novelties. The lack
of true intermediates in the prokaryote to eukaryote
transition has long been a puzzle, but now it is clear
that it has a bioenergetic cause, because prokaryote genome complexity is constrained by membrane bioenergetics [147]. Mitochondria released that constraint and
allowed a growth in genome size and complexity and in
the number of proteins that a cell can express by four
to five orders of magnitude; energy per gene is the key
variable [147,148]. Prokaryotes can readily surpass many
eukaryotes in terms of cell size [149], but they cannot
hold a candle to eukaryotes in terms of true cell complexity. The reason is bioenergetic and boils down to
mitochondria, which are the prerequisite to the origin of
cell complexity – hence phagocytosis – in eukaryotes
[147], not vice versa. On a good day, that would to put
an end to a time-consuming debate regardig the nature
of the host that acquired the mitochondrion: prokaryote
or phagotroph, the recent history of which was readably
summarized by O’Malley [150].
And what about oxygen in eukaryote evolution? Mitochondria afford eukaryotes 10,000 to 100,000 more
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energy per gene [147], while oxygen affords only a factor
of 10-20 [147]. Nonetheless people still seem to think
that the advent of oxygen was a decisive event in eukaryote evolution. We all know that O2 levels limited animal (but not plant) body size during evolution
[151,152]. Under the view of oxygen in Earth history
that was current in the 1980s, the rise of atmospheric
O2 some 2.3 Ga ago was thought to coincide with, and
to have provided causal impetus to, the origin of eukaryotes and mitochondria [153]. But since the mid-1990’s,
a fundamentally different view of Proterozoic ocean
chemistry has emerged from isotope geochemistry. In
the new and current model of Proterozoic ocean chemistry, the O 2 that started accumulating in the atmosphere ~2.3 billion years ago began oxidizing
continental sulfide deposits via weathering [154], carrying very substantial amounts of sulfate into the oceans,
and providing the substrate required for sulfate reducing
prokaryotes, hence fueling marine biological sulfate
reduction (BSR). Marine BSR became a globally significant process, as evidenced by the sedimentary sulfur isotope record [155]. Marine BSR produces marine sulfide
– H 2 S – and lots of it. The presence of that sulfide
means that the oceans were not only sulfidic during that
time, they were also anoxic, both for chemical reasons
and because sulfate reducers are strict anaerobes.
Although the photic zone (the upper 200 meters or so)
was producing oxygen during that time, in the lower
photic zone and below, the oceans were anoxic and sulfidic [156]. Importantly, that anoxic and sulfidic condition persisted until ~580 MY ago, the same time when
the first animal macrofossils appear in the geological
record, with oxygenation of the oceans allowing preexisting and diversified animal lineages to increase in size
[157,158].
As such, eukaryotes, which arose some 1.5 Ga ago
[159], diversified into their major lineages during anoxic
and sulfidic times. It should therefore hardly be surprising (one would think) that diverse eukaryotic lineages
have retained oxygen-independent forms of mitochondrial ATP synthesis from their facultatively anaerobic
common ancestor [127-129,160-162] or that mitochondrial sulfide utilization is widespread among eukaryotic
lineages [163,164]. But the notion that the ability to survive in low oxygen conditions represents a novel and
recent evolutionary achievement of eukaryotes, rather
than an ancient trait, remains popular with some specialists, and lateral gene transfer from one eukaryote lineage to another is suggested as the mechanism
underlying its apparently sparse distribution among
modern lineages [165]. What is disturbing is that exactly
the same kinds of phyletic patterns (patchy distributions
among eukaryote lineages) are usually interpreted not as
LGT but, far more reasonably, as evidence for
Page 12 of 25
differential loss when it comes to structural proteins
[166]. At some point even the staunchest critics of the
view that the presence of anaerobic energy metabolism
in eukaryotes is ancestral will have to admit that anaerobiosis is not an evolutionary achievement of eukaryotes:
it is an ecological specialization. One thinks of Chlamydomonas (a green alga) as an oxygen producer with normal O 2 -respiring mitochondria, but after 30 minutes
under anaerobic conditions in the dark it starts producing the same end-products of energy metabolism as
eukaryotes with hydrogenosomes and using the same
genes and enzymes [167,168]. At face value, the theory
of descent with modification (as opposed to the theory
of lateral transfer) would be a good working hypothesis
to explain that observation. Chlamydomonas does not
have to go out and acquire new genes to survive every
time that oxygen levels drop. Just because prokaryotes
have lots of LGT involved in their genome evolution, we
should not resort to LGT as the default explanation for
the origin of shared traits among eukaryotes, because
the mechanisms of chromosome heredity differ deeply
across the prokaryote-eukaryote divide.
The differences between prokaryotes and eukaryotes
in chromosome heredity provide cause for reflection on
the origin of the cell cycle: eukaryotes have one, prokaryotes do not. The cell cycle is the basis for cell division
and divides the life cycle of a eukaryotic cell into phases
where genes are expressed (always in the presence of a
nucleus, for reasons relating to spliceosomes [134]),
genes are replicated, and genes are distributed among
daughters. In eukaryotes with open mitosis, chromosome segregation occurs in the absence of a nuclear
membrane [132]. The cell cycle requires the full complement of proteins that make eukaryotes complex
[147], hence the cell cycle originated after the origin of
mitochondria. Even in Margulis’s formulations of endosymbiotic theory, the host for the origin of mitochondria
had a nucleus [169]. Related to the cell cycle is the origin of sex, a major transition of early evolution in most
people’s books [24,25,170], one deserving attention from
a fresh perspective.
Conclusion
There is more to evolution than will fit on any tree. For
understanding major transitions in early evolution, we
might not need a tree of life at all. But we need to keep
our ideas testable with data from genomes or other
independent data so as to keep our nose pinned to the
grindstone of observations. The very early evolution of
life is mostly written in the language of chemistry, some
of which is (arguably) still operating today in modern
metabolism if we look at the right groups [171-176].
The environments and starting material that the Earth
had to offer to fuel early chemistry are variables that
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only geochemists can reasonably constrain [30,177,178].
One can make a case that acetogens (clostridial firmicutes) and hydrogenotrophic methanogens (euryarchareotes) harbour the ancestral states of microbial
physiology in the eubacteria and archaebacteria respectively [179], and some trees are compatible with that
view [2,59], as is the distribution of primitive energyconserving mechanisms [51-54]. But given a transition
from the elements on early Earth to replicating cells, the
course of prokaryote evolution does not appear to play
out along the branches of a phylogenetic tree. For example, Whitman [180] surveyed the biology and diversity of
prokaryotes, showing an rRNA tree to discuss matters of
classification; but branching orders in that tree play no
role in his discussion of diversity or underlying evolutionary processes. If that is the direction we are headed
[181], it is not all bad. But having the eukaryotes sitting
on one branch in the rRNA tree of life rather than on
two, as they should be (or three in the case of plants
with their plastids), is far enough off the mark that we
should be striving for a better representation of the relationship of eukaryotes to the two kinds of prokaryotes
from which they stem.
Eukaryotes are genetic chimaeras and the role of mitochondria in the origin of that chimaerism is apparent
[12,103]. Eukaryotes are complex and the pivotal role of
mitochondria in the origin of that complexity (as
opposed to a pivotal role of phagocytosis) seems
increasingly difficult to dispute, for energetic reasons
[147]. That leaves little reasonable alternative to the
view that the host for the origin of mitochondria was a
prokaryote, in the simplest of competing alternatives an
archaebacterium [5]. The antiquity of anaerobic energy
metabolism and sulfide metabolism among eukaryotes
meshes well with newer views of Proterozoic ocean
chemistry [155]. A challenge remains in computing networks of genomes that include lateral gene transfers
among prokaryotes and the origin of eukaryotes in the
same graph. Tracking early evolution without a tree of
life affords far more freedom to explore ideas than
thinking with a tree in hand. The ideas need to generate
predictions and be testable, though, otherwise they are
not science. If we check our thoughts too quickly
against a tree whose truth nobody can determine anyway, the tree begins to decide which thoughts we may
or may not have and which words we may or may not
use. Should a tree of life police our thoughts? Working
without one is an option.
Reviewer report 1
Dan Graur, Department of Biology & Biochemistry,
University of Houston, Houston, TX 77204-5001,
USA
Page 13 of 25
Bill Martin’s timely agitprop raises two unrelated
methodological issues. The first, which impacts the evolution of prokaryotic genomes and the emergence of the
eukaryotic cell, concerns the misuse of binary trees in
cases where the phylogenetic relationships cannot be
described by bifurcations. This problem is not unique to
early evolutionary events. It affects even recent events,
such as the evolution of bread wheat, Triticum aestivum
(an allohexaploid that resulted from two rounds of genome fusion). Such un-binary problems are usually dealt
with by the methodology of phylogenetic networks,
which should be used whenever reticulate events, such
as hybridization, horizontal gene transfer, recombination, fusion, and gene duplication and loss, are believed
to be involved. Indeed, the methodology of networks
has been used in the past by Bill Martin and his collaborators to great effect. Admittedly, the phylogenetic
network methodology is not as yet as mature or as userfriendly as the methodology for producing binary phylogenetic trees, but I regard this obstacle as a minor, easily
remediable, one. Of course, phylogenetic networks, like
phylogenetic trees, will provide neither proximate nor
ultimate causation for the evolutionary occurrences
under study. The phylogenetic networks can only serve
as topological guidelines of the order and relative
importance of the events involved. Beyond the temporal
“buchhalterei,” scientists will require the type of chemical thinking that Bill Martin advocates in his paper.
Author’s response
Thanks for the kind words, one of which required a dictionary, and I agree.
The second issue that Bill Martin raises is infinitely
more difficult to solve. It concerns our ability to deal
with prebiotic systems in which the rules that govern
the process of information transfer from generation to
generation are unknown or even unknowable. Of course,
as scientists we are not suppose to ever declare unknowability, however, in analogy with NP-complete problems
in computer science, we may be mighty close to
unknowability by virtue of the immense number of theoretical possibilities and the limited life expectancy of
scientists and the Earth they inhabit.
Author’s response
The referee is certainly correct that the prebiotic evolution topic is at or, in my view, beyond the limit of what
is knowable. Indeed, endeavours into the origin of life are
unfalsifiable conjecture because even if we constructed a
reactor in the laboratory where chemicals go in on the
one side and newly arisen life (E. coli with d-amino
acids and a different genetic code, for example) pops out
the other, we still wouldn’t have generated ‘proof’of any
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sort that our microbial ancestors arose that way (the
explanandum). We would just have an example that
would make a particular narrative more plausible.
Aware that a heaping helping of unknowability is hard
wired into the problem, we can still pursue the matter
with gusto, knowing that the goal is not to find an
answer, but instead to structure the problem so that we
can talk and write about it in a manner that is meaningful to scientists and to society, which funds our work.
The major problem with dealing with the origin of life
problem is that the boundary conditions are unknown.
We need a framework that will allow us to pursue a
heuristic program of inquiry. Bill Martin takes a big step
in this direction by putting forward a tentative set of
conditions that need to be met for life to emerge.
Among them are redox conditions, compartmentalization, a certain acceptable range of temperatures, a certain acceptable pH range, and the availability of certain
molecules. Furthermore, the prevalence and the locations of sites where such conditions may have existed in
the relevant time frame are identified.
Author’s response
Yes, the boundary conditions are unknown, but if we
consider what sorts of conditions life as we know it (the
only kind whose origin need concern us) demands and
tolerates, then the realm of possible settings for life’s origin takes on some very specific constraints. Coupling that
with what geologists tell us about conditions on the early
Earth constrains the boundary conditions even more.
Origin-of-Life narratives, however, are difficult to evaluate by traditional molecular evolutionists. For example,
the entire edifice of Bill Martin’s approach is based on
the assumption that “life is about redox chemistry.” Will
this proclamation turn out to be more useful in the long
run than Schrödinger’s [182] “life feeds upon negative
entropy"?
Author’s response
“Life is about redox chemisty” leans, of course, on Albert
Szent-Györgyi’s famous but extremely difficult-to-pinpoint quote“ Life is nothing but an electron looking for
a place to rest”. Is this view more useful than Schrödingers’s negentropy? It depends on the meaning of ‘useful’.
Schödinger’s 1944 book is credited with having interested
in biology folks the calibre of François Jacob, Seymour
Benzer, and Maurice Wilkins interested [183]. That level
of utility, for the book, is difficult to surpass. Regarding
the specific concept of negentropy and its utility, the matter is more complicated. Haldane [184]surmised: “The
physiologist who can assimilate the idea of that a living
organism feeds on negative entropy will come back to
the study of metabolism with a slightly novel set of
questions to ask. “ It is probably true that most biologists
Page 14 of 25
who ever learned introductory thermodynamics noticed
right away that life apparently runs contrary to the principle of entropy (increasing disorder). Schrödinger’s inferences that the entropy of live matter is lower than that
of the foodstuffs from which it was formed appear, however, to have some loopholes. For example, Hansen et al.
[185]considered in detail the experimental data on the
differences of energy (ΔG), enthalpy (ΔH), and entropy
(ΔS) between a random arrangement of molecules in
solution and live matter of the same composition, with
the specific goal of rethinking Schrödinger’s negentropy.
They conclude that Schrödinger did not sufficiently specify the reaction for which entropy was to be calculated.
Specifically they suggest that he conflated the energy
required to perform the functions of life (irrelevant to the
calculation of entropy) with the energy required for the
existence of live matter (the thermodynamically relevant
quantity). They argue on the basis of experimental data
that the relevant reaction to consider is:
“mixture of complex molecules in aqueous solution ®
live matter of the same composition”.
They then present considerable experimental evidence
indicating that for that reaction, ΔG, ΔH, and ΔS are all
near zero, an important result that demystifies the
apparent conflict between life and entropy.
Forty years ago, I was convinced that Schrödinger’s
What is Life? held the secret to the origin of life.
Twenty years later, I concluded that Schrödinger contributed nothing to our understanding of life and its origin. I have since become very reluctant to express either
enthusiasm or dislike for any proposal that deals with
problems of life’s origins.
Author’s response
I read Schrödinger’s book only three years ago. It had
almost no influence on me but it is a book that one
should have read. Reluctance and wisdom are often
related, it is probably wise to lack enthusiasm for questions relating to life’s origin.
Paraphrasing Stephen Sondheim, I must summarize
my thoughts thus:
I’ve gotten through Orgel, Oparin and Miller
Gee, that was fun and a half.
When you’ve been through Morowitz
Wickramasinghe,
Anything else is a laugh.
and
Author’s response
I had the memorable pleasure of meeting Harold Morowitz in 2002 and again in 2006. His insights into the
organization of metabolism hold important clues about
biochemical evolution and have had a strong influence
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on my interest in the topic. Perutz complained that
Schrödinger ignored chemistry [183], but no one can say
that about Harold Morowitz.
Reviewer report 2
Ford Doolittle, Biochemistry and Molecular Biology,
Dalhousie University, 5850 College Street, Halifax,
Nova Scotia, Canada B3H 1X5
Not surprisingly, origin and early-evolution-of-life scenarios reflect the disciplinary affiliations of their authors.
Nucleic acid chemists are born RNA-worlders, biochemists worry about metabolism, and phylogeneticists
think the important question is what genes were in the
genome of the last universal common ancestor. Bill
Martin, however, is uniquely polymathic in his
approach, and thus a challenge for this monomathic
reviewer.
Author’s response
Harold Morowitz is a polymath. My approach is narrow
and impatient.
Mostly I will focus on the phylogenetic and genome
evolution aspects of this manuscript. My comments are
however discursive. Commendably, Dr. Martin makes it
clear at the outset that none of us tree-bashers doubts
the basic tree-likeness of the evolution of multicellular
eukaryotes, although incomplete lineage sorting [186]
and hybrid speciation [187]do fuzz the twigs. It seems
still necessary to emphasize “higher eukaryotic” treeness,
and that chimps and bonobos are without any doubt
whatever our surviving sister species, so as not to
encourage those who believe otherwise (and unfortunately they are globally in ascendance). And I heartily
endorse the notion that in abandoning tree-building for
the prokaryotic majority of Life and its history, “we do
not need to worry immediately about the implications
for systematics, which for prokaryotes or phages can
hardly be strictly natural anyway”.
Author’s response
We certainly agree on that...
But, I’d go further to say we really do not need to
worry about prokaryotic systematics at all.
Author’s response
...but we disagree on that, and we have had this discussion before. No tree of life is one thing, no systematics is
quite another. Systematics is defined by some as the
branch of biology that deals with classification and
nomenclature. If the doctor tells us that its Legionella,
that has a meaning with many consequences, whereas
if the doctor cannot tell us what it is (because systematics and nomnclature has been banned), we don’t have
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a clue as to whence the cough. I obviously agree that
we do not need to worry about natural prokaryotic systematics at all; but I maintain that that is fundamentally different from saying that we need no systematics
at all.
Taxa above species are not real things anyway (nor,
with exceptions, are species). For multicellular eukaryotes we have long had to acknowledge that the degree
of phenotypic or genotypic clustering that defines a species, genus, family or whatever varies with the lineage
and the intellectual traditions of those who study it. For
prokaryotes there is this arbitariness and the further
unreality represented by chimerism: there is no unarguably “natural” way to define lineage. And with networks
and the other sorts of data representation now emerging
to deal with LGT, there is anyway no unarguable need
to construct any taxa more inclusive than the isolate.
All we should want to and can know about any organism is how to predict the states of characters X, Y and
Z, given that we know the states of A, B and C. To ask
whether it is a member of some species or larger taxonomic group is to ask a question about how we humans
organize information, not about biological reality. Systematics was anyway just a short cut for predicting
states of X, Y and Z from states of A, B and C, and an
aide-memoire. With all biological information digitized,
who will need it anymore?
Author’s response
At higher levels, prokaryote systematics craters like a
meteorite. At lower levels, who will need prokaryote systematics? Doctors and patients. Why? Because if the doctor wants to prescribe an antibiotic against Legionella,
he has to look in a list that has the query term Legionella, a vocabulary of systematics, in it. To spell Legionella with digital information requires about 43
characters, and Legionella is much easier to remember.
I am not nearly enough a chemist to critique Dr. Martin’s origin scenarios, but too much of a skeptic to
accept his “unquestionably yes” as an answer to the
question “Can we ever understand anything as complex
as the origin of life and early evolution.” This is not
mere defeatism on my part, but loyalty to a sort of uniformitarianism. I think Dr. Martin would agree with me
that the single cellular LUCA to which those who
believe in it would want us to trace all genes - or the
spatiotemporally dispersed population of gene family
cenancestors (each in a different cell) that he and I
would replace it with - was a modern cell (or population), biochemically and molecular biologically and ecologically. Sure, there were times before that when things
were simpler and different, but there is no need to
believe that applying biology’s time-honored principles
of comparison and parsimony will tell us about those
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times. It is possible to believe that, but we don’t need to,
and uniformitarianism legislates against it.
Author’s response
I think the disagreement here has to do with the meaning of “can we ever understand...”. If we let understanding mean the power to make experience intelligible by
applying concepts and categories, which is my intended
meaning, I’ll stand by my ‘yes’. That assent supposes I
take intelligible to mean structuring a problem so that
we can talk about it, which is not what the dictionary
says. Regarding LUCA, I did not bring the concept of a
LUCA into this context or this paper, for the referee’s
reason: it is like talking about happiness. LUCA means
very different things to different people. And how the
heck did uniformitarianism (the same processes operating
in the past as in the present) creep into this? I think that
I am adhering to uniformitarian reasoning in this paper.
It seems to me safer to suppose that all the contemporary world can provide us in terms of information
about origins and early evolution is models. And here
the life from the rocks scenario that Dr. Martin has
developed along with Mike Russell seem very appealing
- though surely underdetermined by the data.
Author’s response
OK.
And I have always worried about the microcompartments seen in vents not serving the role that I think
compartments need to serve, as differentially replicating
targets of natural selection.
Author’s response
Worries on this aspect are unfounded. The inorganic
compartments are territories that can be occupied by
organic contents. Selection operates on the contents, but
the compartments themselves do not need to physically
divide for that selection to occur, obviously. Imagine a
honeycomb that spontaneously grows at the edges (the
growing system of inorganic microcompartments) and a
swarm of parthenogenic bees that lay eggs as fast as they
can (replicating contents) and eat slow egglayers.
Through natural selection, the fastest bees will prevail.
As to the greater complexity of eukaryotes and the
need for mitochondria to underwrite it, I think it cannot
be that simple.
Author’s response
But what if it is that simple? Of all the traits eukaryotic,
which one has the most constructive capability to precipitate the rest? Some have said ‘phagocytosis’ for 40
years, Nick Lane and I say bioenergetics, and specifically
energy per gene. Phagocytosis is a product of complexity,
energy is a prerequisite. One can think of it another way:
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the lack of mitochondria is what has kept prokaryotes
simple.
If I understand what Dr. Martin is saying here, eukaryotes arose in “anoxic and sulfidic times” and we should
not be surprised that “diverse eukaryotic lineages have
retained oxygen-independent forms of mitochondrial
ATP synthesis”, on which those taxa formerly known as
Archezoa once again must rely.
Author’s response
Yes, except that many of them have always relied on
oxygen-independent ATP synthesis. And while the referee
is thinking about microbes, many of the organisms that
have retained the capactiy to thrive in anoxic and sulfidic environments are animals (marine invertebrates for
example).
But then we should be surprised that there are not
eukaryotes that have never enjoyed aerobiosis, never had
full use of their mitochondria, and thus remained forever simple, because they could not take advantage of
this (?) prerequisite to the origin of cell complexity?
Author’s response
Regarding “full use” (oxygen): As explained in Lane and
Martin (2010) mitochondria impart 10,000-100,000
times more energy per gene to their host, whereas oxygen
offers a factor of 20. The “full use” of mitochondria (oxygen) is 500 to 5000 times less important in energetic
terms (the terms that count) than having mitochondria
or not. Put another way, oxygen is only 0.2 to 0.02% as
important as mitochondria when it comes to covering the
energetic costs of evolutionary inventions.
Where are these non-complex eukaryotes? All eukaryotes seem to show pretty much the full meal deal.
Thus, consistent with my comments on another of the
manuscripts in this edition, I think that “fourth domain”
scenarios [188] retain their appeal.
Author’s response
The highly esteemed referee is entitled to enjoy the
appeal of fourth domain models. But why stop at four,
when we can imagine five or six or more? Fourth domain
and similar models (the chronocyte, for example) have
something very much in common with radical versions of
symbiotic theory: Virtually no evolutionary novelty is
attributed to standard evolutionary invention in the history of observable lineages; major novelties are attributed
to acquisition only, in fully fledged form, via symbiotic
mergers. That leaves all the inventing up to lineages
other than the ones that exist, which is problematic. In
Margulis’s versions, we can at least still observe the suspected donors among modern biota (spirochaetes for
example). In contrast, fourth domain scenarios require
all inventors of eukaryotic traits to go extinct shortly
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after one single one of their kind acquired the
mitochondrion.
With all due respect, more distressing with the fourth
domain argument from this particular referee is inconsistency in reasoning. The referee says that are no lineages –
“there is no unarguably “natural” way to define lineage”
above – if we look far enough back in time. Regardless of
whether or not that premise is true, it is assumed to be
true by the referee. A whole fourth domain, a lineage if
there ever was one, and an idealized one at that, is conjured up for the specific purpose of solving a problem
(evolving eukaryotic features) that one could less creatively approach with standard principles of evolutionary
innovation in the ancestors of observable lineages.
How would the referee suggest that the fourth domain
finance, in energetic terms, eukaryotic inventions without
mitochondria? Lane and Martin (2010) might have put
their finger on the sore spot of archezoa and related fourth
domain theories: invention and expression of a genome
complexity with eukaryotic dimension requires mitochondrial power. The lack of true intermediates in the prokaryote-to-eukaryote transition has a bioenergetic cause.
The appearance of the “full meal deal” without leaving
intermediate descendants is far better accounted for in
the wake of mitochondria, than it is under a fourth
domain model, because in the wake of mitochondria, at
least the novelties can be afforded energetically. In the
fourth domain model they cannot, unless we posit that
the fourth domain had some fifth domain mitochondria
in order to become complex before one of its many
lineages (preprochondriates) lost theirs then acquired the
real mitochondria that we see today – too many
assumed lineages, too much imagination.
Thus, I disagree that fourth domain models have much
appeal, other than to those who would contend that
making the leap to the eukaryotic state is asking more
than evolutionary theory has to offer. Fingernails are evolutionary inventions, not acquisitions from a lineage of
free-living fingernails that became symbionts but whose
(n th domain) relatives otherwise became conveniently
extinct. Introns, the spliceosome, the endoplasmic reticulum, et cetera, are also most simply assumed to be
inventions of eukaryotes, not inheritances from extinct
specific-invention-happy donors, until data demand we
reason otherwise.
If we add a fourth domain, then there is no stopping.
We can add more domains and more symbioses at will
to solve each eukaryotic invention problem via acquisition, one symbiosis at a time, which allows too much
freedom (too little constraint) in inferences about the
topic. As regards consistency, we can’t deconstruct everyone else’s lineages and protect only one (the imaginary
fourth) as a host for mitochondria, too.
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Reviewer report 3
Eugene V. Koonin, NCBI, NLM, NIH, Bethesda, MD
20894, USA
This is a very interesting paper (certainly, fantastic
read) that indeed decisively goes beyond the TOL by
effectively dismissing the TOL as either an accurate
depiction of the evolutionary (outside plants and animals) or a useful tool to study evolution. Without going
into much detail, I will state my position on this issue.
Author’s response
Thanks for the kind words, I will try to be terse, too. My
paper deals with more than LGT-ToL, but from the
referees’s upcooming book [170]it seems that we are in
broad and general agreement on the coarse outline of
things regarding origin of life and origin of eukaryote
issues.
As almost all literature in this field, this article argues
against the TOL on the basis of the abundance of “lateral gene transfer” (LGT). And this is I am afraid a contradiction in terms: for any gene transfer to be labelled
lateral, there should be a standard of vertical evolution
to compare it with. If there is none, then there is no
such thing as LGT either, just a tangled web of gene
exchanges. But let us think a little deeper about this and
ask: what are the nodes in that network of life’s evolution? The answer is clear enough: distinct organisms or
groups of organisms or lineages (if one takes the view
that species do not exist among prokaryotes). And of
course we know full well that such lineages exist and
they do exchange genes laterally. What does it mean
that there distinct lineages of prokaryotes (or any organisms)? Ostensibly, that ensembles of genes (genomes)
evolve as coherent, if not immutable, wholes for
extended time intervals. In other words, there are substantial fragments of tree-like evolution in the history of
the prokaryotic world. So far so good but then it is
pointed out that “at depth, the tree of life is not a tree”.
A statement supported by many observations as any
phylogenetic signal certainly deteriorates as one
attempts to trace it back to the early days of life’s history. Still, is it the case that no signal of coherence
between phylogenies of individual genes exists whatsoever? At least one recent study addressed this exact
question, and the answer seems to be that the signal
persists throughout, however weak it is at the deepest
level [189].
Author’s response
Yes, the deeper we go, the weaker the signals get, for several reasons elaborated there [189]. Recalling that folks
can just barely agree on the branching orders for
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mammals (less than 300 MY of evolution) despite abundant homologous molecular data and no LGT that anyone can think of, the existence of any apparent
congruence in the Puigbo et al. NUTs (nearly universal
trees) is actually the surprise, as Leigh et al. [190]show,
the methodological issue of ancient phylogenies notwithstanding [189,191]
So my position is that the TOL is not as dead as it
might seem to be and, if interpreted within a flexible
conceptual framework, it is not an impediment to evolutionary research at all (as repeatedly suggested in this
article). If we reinvent the TOL as a signal of partially
congruent evolution of individual genes and try to measure this trend quantitatively, the answer comes out as
~40% tree-like evolution [16]. This is still a minority of
the evolutionary processes in the prokaryotic world but
a far cry for “a tree of 1%” that the TOL becomes if
interpreted simplistically as the tree of concatenated
universal (see the critique of [2] in [76] and in this article). I think that the “statistical TOL” reflects two
important facets of evolutionary reality:
- A tree is a natural representation of a gene’s history [192] as also acknowledged in this article
- Genes do not evolve in isolation but rather in
ensembles, and there is coherence in the evolution
of such ensembles (genomes) that decays but does
not disappear with evolutionary time.
Author’s response
Yes, genes evolve individually as trees, barring recombination. But I would offer that 40% number needs some
hefty qualification. The 40% number comes from an
analysis of the NUTs [191]. The NUTs, meaning nearly
universal trees, are trees for 102 proteins that are present
in about 90% of broad sample of prokaryotic genomes
[16,189]. Recalling that 102 proteins corresponds to
about 2-3% of typical prokaryotic genome, the 40% number means that about 40% of about 3% of the genome
signal has some vertical component. Forty percent of
three percent boils down to a tree of 1.2% which for our
present purposes is not at all a far cry from a tree of 1%.
We fully agree that towards the tips, prokaryotic evolution is to some extent treelike. But let’s keep in mind
that E. coli has about 18,000 genes [193], of which an
individual only has about 4,500. The concept of “vertical” in situations where an individual only has 25% of
the genes that its species contains requires more qualifications than we want to discuss here.
I believe that the “weak TOL” perceived this way is an
asset to evolutionary biology rather than an impediment,
in part because it is a most convenient - and in my view
legitimate - framework for constructing evolutionary
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scenarios. This position by no account denies the
importance of network representation of evolution as in
[21]. These are not just useful but necessary perspectives
on evolution that are complementary to the tree
perspective.
Author’s response
There is a tree component, and it is at the tips. But my
paper is about early evolution, where today’s tips have
little direct bearing on the issues.
Finally, I would like to make a few notes on the differences between the tree components of evolution in prokaryotes and in eukaryotes. Surely, it is easier to
construct reliable trees for multicellular eukaryotes but
is the difference qualitative or quantitative?
Author’s response
Both, but mostly qualitative.
I would argue for the latter view.
Author’s response
OK, let’s debate this briefly here.
Indeed, even in animals and plants, there are substantial parts of the genomes that hardly show much treelike evolution at any significant phylogenetic depths due
to extensive lineage-specific gene loss and even more
lineage-specific accumulation of mobile elements. Then,
much like in prokaryotes, when one goes deep into the
evolutionary past, the tree signal becomes quite faint:
indeed, no definitive resolution of the relationships
between the eukaryotic supergroups has been reached
despite considerable effort [7,194,195]. The pan-eukaryotic core is not 1% like in prokaryotes but is < 10% of
the gene repertoires of the large genomes. Yes, evolution
of eukaryotes is more tree-like than evolution of prokaryotes (due in large part to meiosis and regular sex in
most groups) but the general description is the same:
the TOL is not an overarching pattern but a statistical
trend and in that form is real and useful.
Author’s response
Right, and in addition euakryotes boast recurrent genome
duplications (ploidization or whole genome duplications)
and quick returns to the original haploid or diploid
genetics via random loss of homeologues [196]. Over
time, that leads to massive hidden microparalogy, a phylogenetic resolution problem specific to eukaryotes
because prokaryotes lack similar mechanisms. And yes,
eukaryote individuals inherit 100%, not 25% of the genes
found in the species, and eukaryotes generally do not
express their genes during cell division, an issue that
relates to the origin of the nucleus, as I think we would
argree. For the purposes of this paper (on early evolution), however, eukaryote phylogeny is an issue of the
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tips, and the tips have a treelike nature, in eukaryotes for
sure: on that we agree. Here the debated point in this
comment is “how much tree is there deep”, and for the
most part my essay says, starting with the title “it doesn’t
really matter”, because none of my arguments are based
on trees (though some might be congruent with aspects
thereof). Given transduction, natural competence, conjugation, gene transfer agents, CRISPRs and the like in prokaryotes vs. “mate with your own kind” inheritance in
eukaryotes, I think it is fair to say the following: the difference is quantitative, as you argue, but it is quantitative for qualitative reasons. Thus, can we agree on a
remis on this point?
Yes, definitely.
Reviewer report 4
Christophe Malaterre
Institut d’Histoire et de Philosophie des Sciences et
Techniques
CNRS
France
It appears that the title of William Martin’s paper only
tells half of the story, namely that part in which it is
very convincingly argued that the concept of a genealogical tree is at best inappropriate - and at worst an
obstacle - for describing the early evolution of life on
Earth (I will call this thesis “argument A”). But there is
another half and that other half consists in two distinct
yet related arguments about first, a hydrothermal origin
of life (argument B), and second, a prokaryote-to-eukaryote transition taking place after the origin of mitochondria (argument C). What really links the three
arguments is their relevance to the early evolution of
life.
Author’s response
Yes.
The paper brings together a wealth of scientific results
on each one of the three arguments and on related
counter-arguments, and shows how they fit together or
do not fit into a larger picture. The article thereby takes
the form of a critical review and provides arguments
that attempt to increase or lower the credibility of some
scientific hypotheses concerning the early evolution of
life over others. This is very convincingly done, in particular for the central argument A.
Author’s response
Thank you.
On a slightly more critical note though, one might
have hoped for a series of converging arguments about
what is supposed to be the thesis of the paper - namely
argument A. Yet, arguments B and C seem to stand
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somehow on their own, each defending a particular
scientific hypothesis, on the origin of life for the first
and on the prokaryote-to-eukaryote transition for the
second. Of course, the paper could be read as a series of
three interconnected theses about early evolution - yet
in this case, the background section in particular would
need to be adjusted accordingly as the objective of the
paper would no longer solely be about the inappropriateness of the tree of life concept for early evolution.
Author’s response
Everyone has their slant on the ToL. In this paper, and
more generally I suppose, my slant is that the role of the
ToL in attempting to understand early evolution is peripheral at best. That this is not to everyone’s taste I
know, and I beg the esteemed referee’s indulgence.
On the other hand, if the objective of the paper is
really about establishing argument A - as suggested by
the title, summary and background sections - it would
be good to show that arguments B and C really contribute to the main argument A, which to a certain extent
they do. Yet in this case a difficulty might be that competing scientific hypotheses about the origin of life and
the prokaryote-to-eukaryote transition than those argued
for in B and C might also be compatible with argument
A: for instance, both scientific hypotheses about the prokaryote-to-eukaryote transition that are argued against
in argument C involve some form of endosymbiosis that
also makes the tree of life concept inappropriate for
depicting the genealogical relationships of the first
microbial organisms. In other words, instead of arguments B and C in their present form, more general
arguments about the existence, during early evolution,
of evolutionary processes distinct from the process of
natural selection (when this one is interpreted in a narrow sense as “heritable variation in fitness”) would fare
as well. In particular, one may argue that any variation
process that would involve heritable material (genetic or
- why not - epigenetic as well) belonging to different
types (or species - if such a concept can be precisely
defined in the context of early evolution) of organisms
would do, from the absorption of small pieces of heritable material (as in the case of lateral gene transfer) to
the complete absorption of organisms (as in the case of
endosymbiosis).
Author’s response
A, B and C are mutually consistent but do not necessarily hinge upon one another. I have no more general
arguments than these to put forth, other than perhaps
the more general argument that chemistry and thermodynamics are important in these issues, which no one in
the de-treeing of life community seems to be saying. That
leaves me standing relatively alone out in left field, I
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reckon, which is fine, unless there is lightning on the
horizon.
In any case, in addition to the three arguments that
are proposed, the paper is thought provoking in many
ways. For me, it also links to the three following questions: (1) What are indeed the evolutionary processes at
work during the period of early evolution beyond that
of natural selection?
Author’s response
Great question. Regarding “process” in the sense that I
think the referee means it (mechanistic cause), I tend to
side with Harold Morowitz here that there is a good portion of contingency built in to the chemistry of life, at
least as far as the synthesis of building blocks go. Morowitz et al. [197]write
“If one wishes to study biogenesis from the bottom up,
the first step is to reason from atoms of the periodic
table to those molecules that form the core of biochemistry, those molecules central to the chart of
intermediary metabolism in chemoautotrophs. [...]
We argue that there is an [...] indication that the
chemistry at the core of the metabolic chart is necessary and deterministic and would likely characterize
any aqueous carbon-based life anywhere it is found
in this universe.”
They wrote that in a paper considering origin of the
the kinds of compounds that are common to central
metabolism in most organisms. Their conclusion is that
chemistry and theromodynamics have the last word. It is
thermodynamics that explains why we observe the same
molecules in for example the citric acid cycle and its variants across modern cells. They say; citric acid cycle
intermediates are not a frozen accident, they are the
kinds of compounds one might expect to see in any form
of life, for reasons intrinsic to the way carbon, oxygen,
and hydrogen tend to form bonds under certain conditions. That is not the same as saying that all molecules
of life should tend to be spontaneously formed, because
much of the chemistry of life is generated by life itself,
not by the environment. The amino acids that constitute
proteins are a case in point, many of them could well
have been the result of biochemical invention [198],
rather than selected from an organic soup.
Might it be the case that processes such as drift [199],
self-organization [200], tinkering [201] or others indeed
prove to be relevant too? (2) What is the relative significance of each one of these evolutionary processes? If
indeed natural selection is not found to be the major
source of evolution during this period, then it implies a
strong conceptual change in the way we tend to think
about evolution (see for instance the relative significance
Page 20 of 25
debate in evolutionary biology [202]). (3) What are the
relationships between these evolutionary processes and
the topology of the genealogical network of the first living organisms? Could it be the case that this topology
might be conditioned by some evolutionary processes
more than by others? And obviously these questions are
not limited to the period of “early evolution” discussed
here: they are naturally relevant to all of evolution,
including what one might call “classic evolution” (see
for instance the discussion about Darwinian populations
[203]) but also the ealier period of “chemical evolution”
that is taken to have preceded that of “early evolution”
[204,205].
Author’s response
Great questions. Drift, self-organization, and tinkering all
have prominent places in evolutionary thinking and
Dyson, Kauffman, and Jacob [199-201]have many
insights on these and other topics. But as far as I can
tell, they are mostly concerned in those works with principles of the type that Beatty [202]also deals with,
namely the interplay between natural selection and
chance processes en route to complexity at one or the
other level. Godfrey-Smith [203]operates in much the
same realm, with special attention to populations as the
unit of selection. Joyce [205]and the RNA world provide
much evidence for the utility of RNA as an information
carrier and a catalyst in the realm of natural selection,
while Calvin’s book [204]for me is the most interesting
among the lot. But how to link any of those thoughts
with conditions on early Earth and real cells as in the
ancestors of the ones we know today? Doolittle did that
a couple of times as best the data available at the time
would allow [188,206], but there was no chemistry or
physiology in any of that; that is, there was no consideration of how the first cells were making a living and how
that related to chemical processes on early Earth.
Dyson [[199], page 53] writes that his mathematical
model “...leaves out all the complicated details of real
organic chemistry.” Mathematics is important, but living
things are not made of equations. They are made of
molecules and the solvent is water. How the heck does
that work and worse, how did it come to be? It requires
carbon and energy, that’s for sure.
Szent Györgyi [207]starts his 1957 book with a question “The problem is: how does energy drive life?”, which
crams quite a big problem into five words, because Szent
Györgyi was looking for chemical and molecular
mechanisms. In chemical evolution, or the transition
from geochemistry to biochemistry, entry to the problem
– for me – involves reading and reasoning one’s way into
what energy releasing reactions on the early Earth might
be homologous to the energy releasing reactions underpinning carbon and energy metabolism in some groups of
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modern cells. For what it’s worth, I do think that the
conections between serpentinization, alkaline hydrothermal vents, accessible electrons in Fe 2+ -containing silicates, CO 2 -reduction, H 2 -production plus CH 4 production at Lost City, and H2-CO2 dependent carbon
and energy metabolism in some methanogenic euryarchaeotes and some acetogenic clostridia, together with the
occurrence of the acetyl-CoA pathway – and now electron bifurcation [51-53]in both groups to conserve energy
through cytosolic pools of soluble reduced iron as ferredoxin – really are telling us something significant about
the nature of the most ancient cells, their ecology, and
their biology. H2 deserves more discussion as a source of
energy for early life.
All that is to say that the questions posed to me by the
referee are too hard to answer: What are the processes?
What is their significance? What are their relationships
to genealogy? I consider it a compliment to have those
questions asked in the context of my essay, but cannot
offer satisfactory answers other than some shorthand
conjecture: The processes are unspectacular energyreleasing chemical reactions driven by the journey of
electrons from serpentinization (Fe 2+ ) and H 2 to CO 2 .
Their significance is that we can, in principle, understand those reactions and relate them to energy and carbon metabolism in some modern groups. Their
relationships to genealogy among the first cells are that
clostridial acetogenesis (eubacteria) and euryarcheal
methanogenesis (archaebecteria) would be the ancestral
states of microbial physiology whereby the universal common ancestor was not a free-living cell.
At any rate, my thanks for the kind and stimulating
comments and I beg the referee’s endulgence, both for my
terse and for my digressive responses.
Minor comments (not for publication)
Page 21 of 25
3.
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9.
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13.
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18.
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20.
Authors’ response
For detecting so many typing and grammar errors, my
sincere gratitude. Thanks very much indeed for such
careful reading.
Acknowledgements
I thank Tal Dagan for discussions, the referees for their time and words, Nick
Lane for additional comments on the paper, and the European Reseach
Council (NETWORKORIGINS), the German Research Foundation and the
Leverhulme Trust for support.
Received: 25 March 2011 Accepted: 30 June 2011
Published: 30 June 2011
References
1. Pagel M: Inferring the historical patterns of biological evolution. Nature
1999, 401:877-884.
2. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, Bork P: Toward
automatic reconstruction of a highly resolved tree of life. Science 2006,
311:1283-1287.
21.
22.
23.
24.
25.
26.
27.
28.
29.
30.
Doolittle WF: Phylogenetic classification and the universal tree. Science
1999, 284:2124-2128.
Treangen TJ, Rocha EPC: Horizontal transfer, not duplication, drives the
expansion of protein families in prokaryotes. PLOS Genetics 2011, 7:
e1001284.
Cox CJ, Foster PG, Hirt RP, Harris SR, Embley TM: The archaebacterial origin
of eukaryotes. Proc Natl Acad Sci USA 2008, 105:20356-20361.
Cotton JA, McInerney JO: Eukaryotic genes of archaebacterial origin are
more important than the more numerous eubacterial genes, irrespective
of function. Proc Natl Acad Sci USA 2010, 107:17252-17255.
Koonin EV: The origin and early evolution of eukaryotes in the light of
phylogenomics. Genome Biol 2010, 11:209.
Bapteste E, O’Malley M, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L,
Lapointe F-J, Dupré J, Dagan T, Boucher Y, Martin W: Prokaryotic evolution
and the tree of life are two different things. Biol Direct 2009, 4:34.
Halary S, Leigh JW, Cheaib B, Lopez P, Bapteste E: Network analyses
structure genetic diversity in independent genetic worlds. Proc Natl Acad
Sci USA 2010, 107:127-132.
Stern A, Sorek R: The phage-host arms race: Shaping the evolution of
microbes. BioEssays 2011, 33:43-51.
McDaniel LD, Young E, Delaney J, Ruhnau F, Ritchie KB, Paul JH: High
frequency of horizontal gene transfer in the oceans. Science 2010, 330:50.
Richards RTA, Archibald JM: Cell evolution: Gene transfer agents and the
origin of mitochondria. Current Biol 2011, 21:R112-R114.
Lane N: Energetics and genetics across the prokaryote-eukaryote divide.
Biol Direct 2011.
Atteia A, Adrait A, Brugière S, van Lis R, Tardif M, Deusch O, Dagan T,
Kuhn L, Gontero B, Martin W, Garin G, Joyard J, Rolland N: A proteomic
survey of Chlamydomonas reinhardtii mitochondria sheds new light on
the metabolic plasticity of the organelle and on the nature of the αproteobacterial mitochondrial ancestor. Mol Biol Evol 2009, 29:1533-1548.
Abhishek A, Bavishi A, Bavishi A, Choudhary M: Bacterial genome
chimaerism and the origin of mitochondria. Can J Microbiol 2011,
57:49-61.
Puigbo P, Wolf YI, Koonin EV: The tree and net components of prokaryote
evolution. Genome Biol Evol 2010, 2:745-756.
Gribaldo S, Poole AM, Daubin V, Forterre P, Brochier-Armanet C: The origin
of eukaryotes and their relationship with the Archaea: are we a
phylogenomic impasse? Nature Rev Microbiol 2010, 8:743-752.
Bapteste E, Susko E, Leigh J, Ruiz-Trillo I, Bucknam J, Doolittle WF:
Alternative methods for concatenation of core genes indicate a lack of
resolution in deep nodes of the prokaryotic phylogeny. Mol Biol Evol
2008, 25:83-91.
Doolittle WF: The practice of classification and the theory of evolution,
and what the demise of Charles Darwin’s tree of life hypothesis means
for both of them. Philos Trans R Soc Lond B Biol Sci 2009, , 364: 2221-2228.
Kunin V, Goldovsky L, Darzentas N, Ouzounis CA: The net of life:
reconstructing the microbial phylogenetic network. Genome Res 2005,
15:954-959.
Dagan T, Artzy-Randrup Y, Martin W: Modular networks and cumulative
impact of lateral transfer in prokaryote genome evolution. Proc Natl Acad
Sci USA 2008, 105:10039-10044.
Popa O, Hazkani-Covo E, Landan G, Martin W, Dagan T: Directed networks
reveal barriers and bypasses to lateral gene traffic among sequenced
prokaryote genomes. Genome Research 2011, 21:599-609.
Lima-Mendez G, Van Helden J, Toussaint A, Leplae R: Reticulate
representation of evolutionary and functional relationships between
phage genomes. Mol Biol Evol 2008, 25:762-777.
Maynard-Smith J, Szathmáry E: The Major Transitions in Evolution Oxford
University Press, Oxford; 1995.
Lane N: Life Ascending: The Ten Great Inventions of Evolution 2009, Profile
Books/Norton.
Koonin EV: The Biological Big Bang model for the major transitions in
evolution. Biology Direct 2007, 2:21.
Haldane JBS: The Orgin of Life. The Rationalist Annual 1929, 3:3-10.
Miller SL: In Major Events in the History of Life. Edited by: Schopf JW. Boston,
Bartlett; 1992:1-28.
Oparin AI: The Origin of Life Dover, New York; 1938.
Russell MJ, Hall AJ: The emergence of life from iron monosulphide
bubbles at a submarine hydrothermal redox and pH front. J Geol Soc
Lond 1997, 154:377-402.
Martin Biology Direct 2011, 6:36
http://www.biology-direct.com/content/6/1/36
31. Martin W, Russell MJ: On the origins of cells: a hypothesis for the
evolutionary transitions from abiotic geochemistry to chemoautotrophic
prokaryotes, and from prokaryotes to nucleated cells. Phil Trans Roy Soc
Lond B 2003, 358:59-85.
32. Martin W, Russell MJ: On the origin of biochemistry at an alkaline
hydrothermal vent. Phil Trans Roy Soc Lond B 2007, 367:1887-1925.
33. Kelley DS, Karson JA, Blackman DK, Früh-Green GL, Butterfield DA, Lilley MD,
Olson EJ, Schrenk MO, Roe KK, Lebon GT, Rivizzigno P: An off-axis
hydrothermal vent field near the Mid-Atlantic Ridge at 30 N. Nature
2001, 412:145-149.
34. Kelley DS, Karson JA, Früh-Green GL, Yoerger DR, Shank TM, Butterfield DA,
Hayes JM, Schrenk MO, Olson EJ, Proskurowski G, Jakuba M, Bradley A,
Larson B, Ludwig K, Glickson D, Buckman K, Bradley AS, Brazelton WJ, Roe ,
Elend MJ, Delacour A, Bernasconi SM, Lilley MD, Baross JA, Summons RE,
Sylva SP: A serpentinite-hosted ecosystem: The Lost City hydrothermal
field. Science 2005, 307:1428-1434.
35. Früh-Green GL, Kelley DS, Bernasconi SM, Karson JA, Ludwig KA,
Butterfield DA, Boschi C: 30,000 years of hydrothermal activity at the Lost
City vent field. Science 2003, 301:495-498.
36. Proskurowski G, Lilley MD, Seewald JS, Früh-Green GL, Olson EJ, Lupton JE,
Sylva SP, Kelley DS: Abiogenic hydrocarbon production at Lost City
Hydrothermal Field. Science 2008, 319:604-607.
37. Baross JA, Hoffman SE: Submarine hydrothermal vents and associated
gradient environments as sites for the origin and evolution of life.
Origins Life Evol Biosphere 1985, 15:327-345.
38. Kelley DS, Baross JA, Delaney JR: Volcanoes, fluids, and life at mid-ocean
ridge spreading centers. Annu Rev Earth Planet Sci 2001, 30:385-491.
39. Martin W, Baross J, Kelley D, Russell MJ: Hydrothermal vents and the
origin of life. Nature Rev Microbiol 2008, 6:805-814.
40. Koonin EV, Martin W: On the origin of genomes and cells within
inorganic compartments. Trends Genet 2005, 21:647-654.
41. Branciamore S, Gallori E, Szathmary E, Czaran T: The origin of life: chemical
evolution of a metabolic system in a mineral honeycomb? J Mol Evol
2009, 69:458-469.
42. Amend JP, McCollom TM: Energetics of biomolecule synthesis on early
Earth. In “Chemical Evolution II: From the Origins of Life to Modern Society”.
Volume Chapter 4. American Chemical Society; 2009:63-94.
43. Brazelton WJ, Ludwig KA, Sogin ML, Andreishcheva EN, Kelley DS, Shen CC,
Edwards RL, Baross JA: Archaea and bacteria with surprising
microdiversity show shifts in dominance over 1,000-year time scales in
hydrothermal chimneys. Proc Natl Acad Sci USA 2010, 107:1612-1617.
44. Stams AJM, Plugge CM: Electron transfer in syntrophic communities of
anaerobic bacteria and archaea. Nature Rev Microbiol 2009, 7:568-577.
45. Amend JP, Shock EL: Energetics of overall metabolic reactions of
thermophilic and hyperthermophilic Archaea and Bacteria. FEMS
Microbiol Rev 2001, 25:175-243.
46. Kaufmann M: On the free energy that drove primordial anabolism. Int J
Mol Sci 2009, 10:1853-1871.
47. Sleep NH, Meibom A, Fridriksson T, Coleman RG, Bird DK: H2-rich fluids
from serpentinization: Geochemical and biotic implications. Proc Natl
Acad Sci USA 2004, 101:12818-12823.
48. Russell MJ, Hall AJ, Martin W: Serpentinization as a source of energy at
the origin of life. Geobiology 2010, 8:355-371.
49. Harold FM: In The Vital Force: A Study of Bioenergetics. Edited by: Freeman
WH. New York; 1986:.
50. Mitchell P: Coupling of phosphorylation to electron and hydrogen
transfer by a chemi-osmotic type of mechanism. Nature 1961,
191:144-148.
51. Herrmann G, Jayamani E, Mai G, Buckel W: Energy conservation via
electron-transferring flavoprotein in anaerobic bacteria. J Bacteriol 2008,
190:784-791.
52. Li F, Hinderberger J, Seedorf H, Zhang J, Buckel W, Thauer RK: Coupled
ferredoxin and crotonyl coenzyme a (CoA) reduction with NADH
catalyzed by the butyryl-CoA dehydrogenase/Etf complex from
Clostridium kluyveri. J Bacteriol 2008, 190:843-850.
53. Kaster A-K, Moll J, Parey K, Thauer RK: Coupling of ferredoxin and
heterodisulfide reduction via electron bifurcation in hydrogenotrophic
mathanogenic archaea. Proc Natl Acad Sci USA 2011, 108:2981-2986.
54. Lane N, Allen JF, Martin W: How did LUCA make a living? Chemiosmosis
and the origin of life. BioEssays 2010, 32:271-280.
Page 22 of 25
55. Wolfe AJ: Physiologically relevant small phosphodonors link metabolism
to signal transduction. Curr Opin Microbiol 2010, 13:204-209.
56. Bradley AS, Summons RE: Multiple origins of methane at the Lost City
Hydrothermal Field. Earth Planetary Sci Lett 2010, 297:34-41.
57. Lang SQ, Butterfield DA, Schulte M, Kelley DS, Lilley MD: Elevated
concentrations of formate, acetate and dissolved organic carbon found
at the Lost City hydrothermal field. Geochim Cosmochim Acta 2010,
74:941-952.
58. Whitman WB, Coleman DC, Wiebe WJ: Prokaryotes: The unseen majority.
Proc Natl Acad Sci USA 1998, 95:6578-6583.
59. Thauer RK, Kaster AK, Seedorf H, Buckel W, Hedderich R: Methanogenic
archaea: ecologically relevant differences in energy conservation. Nature
Rev Microbiol 2008, 6:579-591.
60. Ragsdale SW, Pierce E: Acetogenesis and the Wood-Ljungdahl pathway of
CO2 fixation. Biochim Biophys Acta 2008, 1784:1873-1898.
61. Kopke M, Held C, Hujer S, Liesegang H, Wiezer A, Wollherr A, Ehrenreich A,
Liebl W, Gottschalk G, Durre P: Clostridium ljungdahlii represents a
microbial production platform based on syngas. Proc Natl Acad Sci USA
2010, 107:13087-13092.
62. Biegel E, Muller V: Bacterial Na+-translocating ferredoxin:NAD(+)
oxidoreductase. Proc Natl Acad Sci USA 2010, 107:18138-18142.
63. Thauer RK, Jungermann K, Decker K: Energy conservation in chemotrophic
anaerobic bacteria. Bacteriological Rev 1977, 41:100-180.
64. Kelly S, Wickstead B, Gull K: Archaeal phylogenomics provides evidence in
support of a methanogenic origin of the Archaea and a thaumarchaeal
origin for the eukaryotes. Proc Roy Soc Lond B 2011, 278:1009-1018.
65. Zhaxybayeva O, Swithers KS, Lapierre P, Fournier GP, Bickhart DM,
DeBoy RT, Nelson KE, Nesbø CL, Doolittle WF, Gogarten JP, Noll KM: On the
chimeric nature, thermophilic origin, and phylogenetic placement of the
Thermotogales. Proc Natl Acad Sci USA 2009, 106:5865-5870.
66. Moran JJ, Beal EJ, Vrentas JM, Orphan VJ, Freeman KH, House CH: Methyl
sulfides as intermediates in the anaerobic oxidation of methane. Environ
Microbiol 2008, 10:162-173.
67. Mulkidjanian AY, Galperin MY, Makarova KS, Wolf YI, Koonin EV:
Evolutionary primacy of sodium bioenergetics. Biol Direct 2008, 3:13.
68. Zhidkov I, Livneh EA, Rubin E, Mishmar D: mtDNA mutation pattern in
tumors and human evolution are shaped by similar selective constraints.
Genome Res 2009, 19:576-580.
69. McInerney JO, Cotton JA, Pisani D: The prokaryotic tree of life: Past,
present...and future? Trends Ecol Evol 2008, 23:276-281.
70. Lang AS, Beatty JT: Importance of widespread gene transfer agent genes
in alpha-proteobacteria. Trends Microbiol 2007, 15:54-62.
71. Moran NA: Symbiosis as an adaptive process and source of phenotypic
complexity. Proc Natl Acad Sci USA 2007, 104:8627-8633.
72. Thomas CM, Nielsen KM: Mechanisms of, and barriers to, horizontal gene
transfer between bacteria. Nat Rev Microbiol 2005, 3:711-721.
73. Delsuc F, Brinkmann H, Philippe H: Phylogenomics and the reconstruction
of the tree of life. Nat Rev Genet 2005, 6:361-375.
74. Raymond J, Zhaxybayeva O, Gogarten JP, Gerdes SY, Blankenship RE:
Whole-genome analysis of photosynthetic prokaryotes. Science 2002,
298:1616-1620.
75. Nakamura Y, Itoh T, Matsuda H, Gojobori T: Biased biological functions of
horizontally transferred genes in prokaryotic genomes. Nat Genet 2004,
36:760-766.
76. Dagan T, Martin W: The tree of one percent. Genome Biol 2006, 7:118.
77. Alon U: Network motifs: theory and experimental approaches. Nat Rev
Genet 2007, 8:450-461.
78. Pal C, Papp B, Lercher MJ: Adaptive evolution of bacterial metabolic
networks by horizontal gene transfer. Nat Genet 2005, 37:1372-1375.
79. Jeong H, Mason SP, Barabasi AL, Oltvai ZN: Lethality and centrality in
protein networks. Nature 2001, 411:41-42.
80. Huson DH, Bryant D: Application of phylogenetic networks in
evolutionary studies. Mol Biol Evol 2006, 23:254-267.
81. Huson DH, Scornavacca C: A survey of combinatorial methods for
phylogenetic networks. Genome Biol Evol 2010, 3:23-35.
82. Rezende EL, Lavabre JE, Guimaraes PR, Jordano P, Bascompte J: Nonrandom coextinctions in phylogenetically structured mutualistic
networks. Nature 2007, 448:925-928.
83. Fournier GP, Gogarten JP: Rooting the ribosomal tree of life. Mol Biol Evol
2010, 27:1792-1801.
Martin Biology Direct 2011, 6:36
http://www.biology-direct.com/content/6/1/36
84. Kloesges T, Popa O, Martin W, Dagan T: Networks of gene sharing among
329 proteobacterial genomes reveal differences in lateral gene transfer
frequency at different phylogenetic depths. Mol Biol Evol 2011,
28:1057-1074.
85. Dagan T, Roettger M, Bryant D, Martin W: Genome networks root the tree
of life between prokaryotic domains. Genome Biol Evol 2010, 2:379-392.
86. O’Malley MA, Martin W, Dupre J: The tree of life: introduction to an
evolutionary debate. Biol Philos 2010, 25:441-453.
87. Doolittle WF: The attempt on the life of the Tree of Life: science,
philosophy and politics. Biol Philos 2010, 25:455-473.
88. Rieppel O: The series, the network, and the tree: changing metaphors of
order in nature. Biol Philos 2010, 25:475-496.
89. O’Malley MA: Ernst Mayr, the tree of life, and philosophy of biology. Biol
Philos 2010, 25:529-552.
90. Lawrence JG, Retchless AC: The myth of bacterial species and speciation.
Biol Philos 2010, 25:569-588.
91. Andam CP, Williams D, Gogarten JP: Natural taxonomy in light of
horizontal gene transfer. Biol Philos 2010, 25:589-602.
92. Bouchard F: Symbiosis, lateral function transfer and the many saplings of
life. Biol Philos 2010, 25:623-641.
93. Malaterre C: Lifeness signatures and the roots of the tree of life. Biol
Philos 2010, 25:643-658.
94. Beiko RG: Gene sharing and genome evolution: networks in trees and
trees in networks. Biol Philos 2010, 25:659-673.
95. Velasco JD, Sober E: Testing for treeness: lateral gene transfer,
phylogenetic inference, and model selection. Biol Philos 2010, 25:675-687.
96. Franklin-Hall LR: Trashing life’s tree. Biol Philos 2010, 25:689-709.
97. Bapteste E, Burian RM: On the need for integrative phylogenomics, and
some steps toward its creation. Biol Philos 2010, 25:711-736.
98. Martin W: Is something wrong with the tree of life? BioEssays 1996,
18:523-527.
99. Martin W: Mosaic bacterial chromosomes–a challenge en route to a tree
of genomes. BioEssays 1999, 21:99-104.
100. Saap J: The New Foundations of Evolution: On the Tree of Life Oxford
University Press, Oxford; 2009.
101. Cummins C, McInerney JO: A method for inferring the rate of evolution
of homologous characters that can potentially improve phylogenetic
inference, resolve deep divergence and correct systematic biases. Syst
Biol 2011.
102. Rivera MC, Jain R, Moore JE, Lake JA: Genomic evidence for two
functionally distinct gene classes. Proc Natl Acad Sci USA 1998,
95:6239-6244.
103. Pisani D, Cotton JA, McInerney JO: Supertrees disentangle the chimerical
origin of eukaryotic genomes. Mol Biol Evol 2007, 24:1752-1760.
104. Martin W, Hoffmeister M, Rotte C, Henze K: An overview of endosymbiotic
models for the origins of eukaryotes, their ATP-producing organelles
(mitochondria and hydrogenosomes), and their heterotrophic lifestyle.
Biol Chem 2001, 382:1521-1539.
105. Cavalier-Smith T: The neomuran origin of archaebacteria, the
negibacterial root of the universal tree and bacterial megaclassification.
Int J Syst Evol Microbiol 2002, 52:7-76.
106. Cavalier-Smith T: The phagotrophic origin of eukaryotes and
phylogenetic classification of Protozoa. Int J Syst Evol Microbiol 2002,
52:297-354.
107. Cavalier-Smith T: Origin of the cell nucleus, mitosis and sex: roles of
intracellular coevolution. Biol Direct 2010, 5:7.
108. Cavalier-Smith T: The origin of nuclei and of eukaryotic cells. Nature 1975,
256:463-468.
109. Stanier Y: Some aspects of the biology of cells and their possible
evolutionary significance. Symp Soc Gen Microbiol 1970, 20:1-38.
110. de Duve C: The origin of eukaryotes: A reappraisal. Nat Rev Genet 2007,
8:395-403.
111. Cavalier-Smith T: Archaebacteria and Archezoa. Nature 1989, 339:100-101.
112. Lake JA, Rivera MC: Was the nucleus the first endosymbiont? Proc Natl
Acad Sci USA 1994, 91:2880-2881.
113. Gupta RS, Golding GB: The origin of the eukaryotic cell. Trends Biochem Sci
1996, 21:166-171.
114. Emelyanov VV: Mitochondrial connection to the origin of the eukaryotic
cell. Eur J Biochem 2003, 270:1599-1618.
Page 23 of 25
115. Horiike T, Hamada K, Miyata D, Shinozawa T: The origin of eukaryotes is
suggested as the symbiosis of Pyrococcus into γ-proteobacteria by
phylogenetic tree based on gene content. J Mol Evol 2004, 59:606-619.
116. Moreira D, Lopez-Garcia P: Symbiosis between methanogenic archaea
and δ-proteobacteria as the origin of eukaryotes: the syntrophic
hypothesis. J Mol Evol 1998, 47:517-530.
117. Lopez-Garcia P, Moreira D: Metabolic symbiosis at the origin of
eukaryotes. Trends Biochem Sci 1999, 24:88-93.
118. Moreira D, Ranjard L, Lopez-Garcia P: The nucleolar proteome and the
(endosymbiotic) origin of the nucleus. BioEssays 2004, 26:1144-1145.
119. Forterre P: A new fusion hypothesis for the origin of Eukarya: better than
previous ones, but probably also wrong. Res Microbiol 2011, 162:77-91.
120. Martin W: Archaebacteria (Archaea) and the origin of the eukaryotic
nucleus. Curr Opin Microbiol 2005, 8:630-637.
121. Jekely G, Arendt D: Evolution of intraflagellar transport from coated
vesicles and autogenous origin of the eukaryotic cilium. Bioessays 2006,
28:191-198.
122. Gabaldon T, Snel B, van Zimmeren F, Hemrika W, Tabak H, Huynen MA:
Origin and evolution of the peroxisomal proteome. Biol Direct 2006, 1:8.
123. Tovar J, Fischer A, Clark CG: The mitosome, a novel organelle related to
mitochondria in the amitochondrial parasite Entamoeba histolytica. Mol
Microbiol 1999, 32:1013-1021.
124. Williams BA, Hirt RP, Lucocq JM, Embley TM: A mitochondrial remnant in
the microsporidian Trachipleistophora hominis. Nature 2002, 418:865-869.
125. Tovar J, León-Avila G, Sánchez LB, Sutak R, Tachezy J, van der Giezen M,
Hernández M, Müller M, Lucocq JM: Mitochondrial remnant organelles of
Giardia function in iron-sulphur protein maturation. Nature 2003,
426:172-176.
126. Hrdy I, Hirt RP, Dolezal P, Bardonova L, Foster PG, Tachezy J, Embley TM:
Trichomonas hydrogenosomes contain the NADH dehydrogenase
module of mitochondrial complex I. Nature 2004, 432:618-622.
127. Tielens AGM, Rotte C, van Hellemond JJ, Martin W: Mitochondria as we
don’t know them. Trends Biochem Sci 2002, 27:564-572.
128. van der Giezen M: Hydrogenosomes and mitosomes: Conservation and
evolution of functions. J Euk Microbiol 2009, 56:221-231.
129. Embley TM, Martin W: Eukaryote evolution: changes and challenges.
Nature 2006, 440:623-630.
130. Searcy DG: Origins of mitochondria and chloroplasts from sulphur-based
symbioses. In The Origin and Evolution of the Cell. Edited by: Hartman H,
Matsuno K. World Scientific, Singapore; 1992:47-78.
131. Vellai T, Takacs K, Vida G: A new aspect to the origin and evolution of
eukaryotes. J Mol Evol 1998, 46:499-507.
132. Martin W, Müller M: The hydrogen hypothesis for the first eukaryote.
Nature 1998, 392:37-41.
133. Martin W, Brinkmann H, Savona C, Cerff R: Evidence for a chimaeric nature
of nuclear genomes: Eubacterial origin of eukaryotic glyceraldehyde-3phosphate dehydrogenase genes. Proc Natl Acad Sci USA 1993,
90:8692-8696.
134. Martin W, Koonin EV: Introns and the origin of nucleus-cytosol
compartmentation. Nature 2006, 440:41-45.
135. Leclercq S, Giraud I, Cordaux R: Remarkable abundance and evolution of
mobile group II introns in Wolbachia bacterial endosymbionts. Mol Biol
Evol 2011, 28:685-697.
136. Chalamcharla VR, Curcio MJ, Belfort M: Nuclear expression of a group II
intron is consistent with spliceosomal intron ancestry. Genes Dev 2010,
24:827-836.
137. Kleine T, Maier UG, Leister D: DNA transfer from organelles to the
nucleus: the idiosyncratic genetics of endosymbiosis. Annu Rev Plant Biol
2009, , 60: 115-138.
138. Hazkani-Covo E, Zeller RM, Martin W: Molecular poltergeists: mitochondrial
DNA copies (numts) in sequenced nuclear genomes. PLoS Genet 2010, 6:
e1000834.
139. von Dohlen CD, Kohler S, Alsop ST, McManus WR: Mealybug βproteobacterial symbionts contain γ-proteobacterial symbionts. Nature
2001, 412:433-436.
140. Yutin N, Wolf MY, Wolf YI, Koonin EV: The origins of phagocytosis and
eukaryogenesis. Biol Direct 2009, 4:9.
141. Poole A, Nadja Neumann N: Reconciling an archaeal origin of eukaryotes
with engulfment: a biologically plausible update of the Eocyte
hypothesis. Res Microbiol 2011, 162:71-76.
Martin Biology Direct 2011, 6:36
http://www.biology-direct.com/content/6/1/36
142. Minerdi D, Bianciotto V, Bonfante P: Endosymbiotic bacteria in mycorrhizal
fungi: from their morphology to genomic sequences. Plant Soil 2002,
244:211-219.
143. Kobayashi DY, Crouch JA: Bacterial/fungal interactions: from pathogens to
mutualistic endosymbionts. Annu Rev Phytopathol 2009, 47:63-82.
144. Forterre P, Gribaldo S: Bacteria with a eukaryotic touch: A glimpse of
ancient evolution? Proc Natl Acad Sci USA 2010, 107:12739-12740.
145. Forterre P, Philippe H: Where is the root of the universal tree of life?
BioEssays 1999, 21:871-879.
146. Makarova KS, Wolf YI, Mekhedov SL, Mirkin BG, Koonin EV: Ancestral
paralogs and pseudoparalogs and their role in the emergence of the
eukaryotic cell. Nucleic Acids Res 2005, 33:4626-4638.
147. Lane N, Martin W: The energetics of genome complexity. Nature 2010,
467:929-934.
148. Allen JF: The function of genomes in bioenergetic organelles. Phil Trans
Roy Soc Lond B 2003, 358:19-37.
149. Mendell JE, Clements KD, Choat JH, Angert ER: Extreme polyploidy in a
large bacterium. Proc Natl Acad Sci USA 2008, 105:6730-6734.
150. O’Malley MA: The first eukaryote cell: an unfinished history of
contestation. Studies Histor Philos Biol Biomed Sci 2010, 41:212-224.
151. Payne JL, McClain CR, Boyer AG, Brown JH, Finnegan S, Kowalewski M,
Krause RA Jr, Lyons SK, McShea DW, Novack-Gottshall PM, Smith FA,
Spaeth P, Stempien JA, Wang SC: The evolutionary consequences of
oxygenic photosynthesis: a body size perspective. Photosynth Res 2011,
107:37-57.
152. Danovaro R, Dell’ Anno A, Pusceddu A, Gambi C, Heiner I, Kristensen RM:
The first metazoa living in permanently anoxic coditions. BMC Biology
2010, 8:30.
153. Walker JC, Margulis L, Rambler M: Reassessment of roles of oxygen and
ultraviolet light in Precambrian evolution. Nature 1976, 264:620-624.
154. Poulton SW, Fralick PW, Canfield DE: The transition to a sulphidic ocean
~1.84 billion years ago. Nature 2004, 431:173-177.
155. Lyons TW, Anbar AD, Severmann S, Scott C, Gill BC: Tracking euxinia in the
ancient ocean: A multiproxy perspective and proterozoic case study.
Annu Rev Earth Planet Sci 2009, 37:507-534.
156. Johnston DT, Wolfe-Simon F, Pearson A, Knoll AH: Anoxygenic
photosynthesis modulated Proterozoic oxygen and sustained Earth’s
middle age. Proc Natl Acad Sci USA 2009, 106:16925-16929.
157. Fike DA, Grotzinger JP, Pratt LM, Summons RE: Oxidation of the Ediacaran
ocean. Nature 2006, 444:744-747.
158. Shen B, Dong L, Xiao SH, Kowalewski M: The Avalon explosion: Evolution
of Ediacara morphospace. Science 2008, 319:81-84.
159. Javaux EJ, Knoll AH, Walter MR: Morphological and ecological complexity
in early eukaryotic ecosystems. Nature 2001, 412:66-69.
160. Ginger ML, Fritz-Laylin LK, Fulton C, Cande WZ, Dawson SC: Intermediary
metabolism in protists: a sequence-based view of facultative anaerobic
metabolism in evolutionarily diverse eukaryotes. Protist 2010,
161:642-671.
161. Dietrich LEP, Tice MM, Newman DK: The co-evolution of life and Earth.
Curr Biol 2006, 16:R395-R400.
162. Mentel M, Martin W: Energy metabolism among eukaryotic anaerobes in
light of Proterozoic ocean chemistry. Phil Trans Roy Soc Lond B 2008,
363:2717-2729.
163. Theissen U, Hoffmeister M, Grieshaber M, Martin W: Single eubacterial
origin of eukaryotic sulfide:quinone oxidoreductase, a mitochondrial
enzyme conserved from the early evolution of eukaryotes during anoxic
and sulfidic times. Mol Biol Evol 2003, 20:1564-1574.
164. Theissen U, Martin W: Sulfide:quinone oxidoreductase (SQR) from the
lugworm Arenicola marina shows cyanide- and thioredoxin-dependent
activity. FEBS J 2008, 257:1131-1139.
165. Stairs CW, Roger AJ, Hampl H: Eukaryotic pyruvate formate lyase and its
activating enzyme were acquired laterally from a firmicute. Mol Biol Evol
2011.
166. Sebe-Pedros A, Roger AJ, Lang FB, King N, Ruiz-Trillo I: Ancient origin of
the integrin-mediated adhesion and signaling machinery. Proc Natl Acad
Sci USA 2010, 107:10142-10147.
167. Mus F, Dubini A, Seibert M, Posewitz MC, Grossman AR: Anaerobic
acclimation in Chlamydomonas reinhardtii anoxic gene expression,
hydrogenase induction, and metabolic pathways. J Biol Chem 2007,
282:25475-25486.
Page 24 of 25
168. Meuser JE, Ananyev G, Wittig LE, Kosourov S, Ghirardi ML, Seibert M,
Dismukes GC, Posewitz MC: Phenotypic diversity of hydrogen production
in chlorophycean algae reflects distinct anaerobic metabolisms. J Biotech
2009, 142:21-30.
169. Margulis L, Dolan MF, Guerrero R: The chimeric eukaryote: Origin of the
nucleus from the karyomastigont in amitochondriate protists. Proc Natl
Acad Sci USA 2000, 97:6954-6959.
170. Koonin EV: The Logic of Chance: The Nature and Origin of Biological Evolution
FT Press, Upper Saddle River, New Jersey; 2011.
171. Fuchs G, Stupperich E: Evolution of autotrophic CO2 fixation. In Evolution
of prokaryotes. Edited by: Schleifer KH, Stackebrandt E. London, UK:
Academic Press; 1985:235-251, FEMS Symposium No. 29.
172. Ferry JG, House CH: The step-wise evolution of early life driven by
energy conservation. Mol Biol Evol 2006, 23:,1286-1292.
173. Ljungdahl LG: A life with acetogens, thermophiles, and cellulolytic
anaerobes. Annu Rev Microbio 2009, 63:1-25.
174. Ragsdale SW: Nickel-based enzyme systems. J Biol Chem 2009,
284:18571-18575.
175. Berg IA: Ecological aspects of the distribution of different autotrophic
CO2 fixation pathways. Appl Environ Microbiol 2011, 77:1925-1936.
176. Berg IA, Kockelkorn D, Ramos-Vera WH, Say RF, Zarzycki J, Hugler M,
Alber BE, Fuchs G: Autotrophic carbon fixation in archaea. Nature Rev
Microbiol 2010, 8:447-460.
177. Ducluzeau AL, van Lis R, Duval S, Schoepp-Cothenet B, Russell MJ,
Nitschke W: Was nitric oxide the first deep electron sink? Trend Biochem
Sci 2009, 34:9-15.
178. Russell MJ: The hazy details of early Earth’s atmosphere. Science 2010,
330:754.
179. Martin W: On the ancestral state of microbial physiology. In Life Strategies
of Microorganisms in the Environment and in Host Organisms Nova Acta
Leopoldina Edited by: Amann R, Goebel W, Schink B, Widdel F 2008,
96:53-60.
180. Whitman EB: The modern concept of the procaryote. J Bact 2009,
191:2000-2005.
181. Doolittle WF, Bapteste E: Pattern pluralism and the Tree of Life
hypothesis. Proc Natl Acad Sci USA 2007, 104:2043-2049.
182. Schrödinger E: What is Life? Cambridge University Press, Cambridge; 1944.
183. Perutz M: Physics and the riddle of life. Nature 1987, 326:555-558.
184. Haldane JBS: A physicist looks at genetics. Nature 1945, 155:375-376.
185. Hansen LD, Criddle RS, Battley EH: Biological calorimetry and the
thermodynamics of the origination and evolution of life. Pure Appl Chem
2009, 81:1843-1855.
186. Maddison WP, Knowles LL: Inferring phylogeny despite incomplete
lineage sorting. Syst Biol 2006, 55:21-30.
187. Mallett J: Hybrid speciation. Nature 2007, 446:279-283.
188. Darnell JE, Doolittle WF: Speculations on the early course of evolution.
Proc Natl Acad Sci USA 1986, 83:1271-1275.
189. Puigbo P, Wolf YI, Koonin EV: Search for a ‘tree of life’ in the thicket of
the phylogenetic forest. J Biol 8:59.
190. Leigh JW, Schliep K, Lopez P, Bapteste E: Let them fall where they may:
Congruence analysis in massive, phylogenetically messy datasets. Mol
Biol Evol 2011.
191. Ané C: Detecting phylogenetic breakpoints and discordance from
genome-wide alignments for species tree reconstruction. Genome Biol
Evol 2011, 3:246-258.
192. Koonin EV, Wolf YI: The fundamental units, processes and patterns of
evolution, and the tree of life conundrum. Biol Direct 2009, 4:33.
193. Lukjancenko O, Wassenaar TM, Ussery DW: Comparison of 61 sequenced
Escherichia coli genomes. Microb Ecol 2010, 60:708-720.
194. Keeling PJ: Genomics. Deep questions in the tree of life. Science 2007,
317:1875-1876.
195. Hampl V, Hug L, Leigh JW, Dacks JB, Lang BF, Simpson AGB, Roger AJ:
Phylogenomic analyses support the monophyly of Excavata and resolve
relationships among eukaryotic “supergroups”. Proc Natl Acad Sci USA
2009, 106:3859-3864.
196. Scannell DR, Byrne KP, Gordon JL, Wong S, Wolfe KH: Multiple rounds of
speciation associated with reciprocal gene loss in polyploid yeasts.
Nature 2006, 440:341-345.
197. Morowitz HJ, Kostelnik JD, Yang J, Cody GD: The origin of intermediary
metabolism. Proc Natl Acad Sci USA 2000, 97:7704-7708.
Martin Biology Direct 2011, 6:36
http://www.biology-direct.com/content/6/1/36
Page 25 of 25
198. Copley SD, Smith E, Morowitz HJ: A mechanism for the association of
amino acids with their codons and the origin of the genetic code. Proc
Natl Acad Sci USA 2005, 102:4442-4447.
199. Dyson F: Origins of Life Cambridge: Cambridge University Press; 1985.
200. Kauffman S: The Origins of Order: Self-Organization and Selection in Evolution
New York: Oxford University Press; 1993.
201. Jacob F: Evolution and Tinkering. Science 1977, 196:1161-1166.
202. Beatty J: Chance and natural selection. Philosophy of Science 1984,
51:183-211.
203. Godfrey-Smith P: Darwinian Populations and Natural Selection Oxford:
Oxford University Press; 2009.
204. Calvin M: Chemical Evolution: Molecular Evolution Towards the Origin of Life
on the Earth and Elsewhere New York: Oxford University Press; 1969.
205. Joyce G: The antiquity of RNA-based evolution. Nature 2002, 418:214-221.
206. Doolittle WF, Brown JR: Tempo, mode, the progenote, and the universal
root. Proc Natl Acad Sci USA 2004, 91:6721-6728.
207. Szent Györgyi A: Bioenergetics Academic Press, New York; 1957.
doi:10.1186/1745-6150-6-36
Cite this article as: Martin: Early evolution without a tree of life. Biology
Direct 2011 6:36.
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